diff --git a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2PRISM.java b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2PRISM.java
index d3704d084..234565457 100644
--- a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2PRISM.java
+++ b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2PRISM.java
@@ -18,10 +18,12 @@ import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
-
+import java.util.Map;
 
 import org.sbml.jsbml.Compartment;
+import org.sbml.jsbml.LocalParameter;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.Parameter;
 import org.sbml.jsbml.Reaction;
@@ -31,7 +33,6 @@ import org.sbml.jsbml.SpeciesReference;
 
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
 
-
 /**
  * Perform conversion from SBML to PRISM.
  *
@@ -57,8 +58,8 @@ public class SBML2PRISM {
 	 * conversion/target/iBioSim-conversion-3.1.0-SNAPSHOT-jar-with-dependencies.jar
 	 * -l PRISM YOURSBMLFILE.xml
 	 * 
-	 * The function also allows the translation into a bound model by simply adding the flag 
-	 * -bound
+	 * The function also allows the translation into a bound model by simply adding
+	 * the flag -bound
 	 */
 
 	public static void convertSBML2PRISM(SBMLDocument sbmlDoc, String filename, boolean unbound) throws IOException {
@@ -73,181 +74,356 @@ public class SBML2PRISM {
 		out.write("\n");
 		out.write("ctmc\n");
 		out.write("\n");
-		
+
 		// Set bound limit if bound model is selected
-		if (unbound) {
-			out.write("// const int MAX_AMOUNT = ADD VALUE \n");
-			out.write("\n");
-		} else {
-			double maxAmount = 0.0;
-			for (int i = 0; i < model.getSpeciesCount(); i++) {
-				Species species = model.getSpecies(i);
-				if (species.getInitialAmount() > maxAmount) {
-					maxAmount = species.getInitialAmount();
-				}
-			}
-			out.write(" const int MAX_AMOUNT = " + (int) maxAmount + ";\n");
-			out.write("\n");				out.write("\n");
+		if (!unbound) {
+
+			System.err.println("Under Development");
+			/*
+			 * double maxAmount = 0.0; for (int i = 0; i < model.getSpeciesCount(); i++) {
+			 * Species species = model.getSpecies(i); if (species.getInitialAmount() >
+			 * maxAmount) { maxAmount = species.getInitialAmount(); } }
+			 * out.write(" const int MAX_AMOUNT = " + (int) maxAmount + ";\n");
+			 */
 		}
 
-		
-		// Identify compartments and their size
-		out.write("// Compartment size\n");
+		// Declaration of new Compartment list
+		ArrayList<Compartment> compartmentList = new ArrayList<Compartment>();
 
+		// Iterating over Compartments
 		for (int i = 0; i < model.getCompartmentCount(); i++) {
 			Compartment compartment = model.getCompartment(i);
-			out.write("const double " + checkReservedKeywordPrism(compartment.getId()) + " = " + compartment.getSize()
-					+ ";\n");
+			compartmentList.add(compartment);
 		}
 
-		out.write("\n");
+		// System.err.println("Compartment List: " + compartmentList + "\n");
+
+		// Identify compartments and their size
+		if (!compartmentList.isEmpty()) {
+			out.write("// Compartment size\n");
+		}
+
+		for (int i = 0; i < compartmentList.size(); i++) {
+			String id = checkReservedKeywordPrism(compartmentList.get(i).getId());
+			// System.err.println("Id: " + id);
+			Double size = compartmentList.get(i).getSize();
+			// System.err.println("Size: " + size);
+			if (!Double.isNaN(size)) {
+				out.write("const double " + id + " = " + size + ";\n");
+			}
+		}
 
 		// Identify model parameters
-		out.write("// Model parameters\n");
+		// Declaration of new parameter list
+		ArrayList<Parameter> parameterList = new ArrayList<Parameter>();
 
+		// Iterating over Compartments
 		for (int i = 0; i < model.getParameterCount(); i++) {
 			Parameter parameter = model.getParameter(i);
-			out.write("const double " + checkReservedKeywordPrism(parameter.getId()) + " = " + parameter.getValue()
-					+ "; // " + parameter.getName() + "\n"); // if not null name
+			parameterList.add(parameter);
+		}
+
+		// System.err.println("Parameter List: " + parameterList + "\n");
+
+		if (!parameterList.isEmpty()) {
+			out.write("\n");
+			out.write("// Model parameters\n");
+		}
+
+		for (int i = 0; i < parameterList.size(); i++) {
+			String id = checkReservedKeywordPrism(parameterList.get(i).getId());
+			Double value = parameterList.get(i).getValue();
+			String name = parameterList.get(i).getName();
+
+			if (!Double.isNaN(value)) {
+				out.write("const double " + id + " = " + value + "; // " + name + "\n"); // if not null name
+			}
+		}
+
+		// Identify reactions
+		// Declaration of new reaction list
+		ArrayList<Reaction> reactionList = new ArrayList<Reaction>();
+		// Iterating over reactions
+		for (int i = 0; i < model.getReactionCount(); i++) {
+			Reaction reaction = model.getReaction(i);
+			reactionList.add(reaction);
+		}
+
+		// System.err.println("Reaction List: " + reactionList + "\n");
+
+		// Identify local model parameters
+		// Declaration of new local parameter list
+		ArrayList<LocalParameter> localParameterList = new ArrayList<LocalParameter>();
+		// Iterating over local parameters
+		for (int i = 0; i < reactionList.size(); i++) {
+			for (int j = 0; j < reactionList.get(i).getKineticLaw().getLocalParameterCount(); j++) {
+				LocalParameter localparameter = reactionList.get(i).getKineticLaw().getLocalParameter(j);
+				localParameterList.add(localparameter);
+			}
+		}
+
+		// while (localParameterList.remove(null));
+		// System.err.println("LocalParameterList: " + localParameterList + "\n");
+
+		ArrayList<LocalParameter> UpdatedlocalParameterList = new ArrayList<LocalParameter>();
+		for (int i = 0; i < reactionList.size(); i++) {
+			for (int j = 0; j < reactionList.get(i).getKineticLaw().getLocalParameterCount(); j++) {
+				LocalParameter localparameter = reactionList.get(i).getKineticLaw().getLocalParameter(j);
+				// System.err.println("localparameter: " + localparameter);
+				if (localparameter != null) {
+					if (localParameterList.contains(localparameter)) {
+						reactionList.get(i).getKineticLaw().getLocalParameter(j)
+								.setId("local_" + localparameter.getId() + "_" + i);
+						// System.err.println(
+						// "localparameter: " + reactionList.get(i).getKineticLaw().getLocalParameter(j)
+						// + "\n");
+						UpdatedlocalParameterList.add(reactionList.get(i).getKineticLaw().getLocalParameter(j));
+					}
+				}
+			}
+		}
+
+		for (int i = 0; i < reactionList.size(); i++) {
+			for (int j = 0; j < reactionList.get(i).getKineticLaw().getLocalParameterCount(); j++) {
+				// System.err.println("Reaction local parameter updated: "
+				// + reactionList.get(i).getKineticLaw().getLocalParameter(j));
+			}
+		}
+
+		if (!UpdatedlocalParameterList.isEmpty()) {
+			out.write("\n");
+			out.write("// Model local parameters\n");
+		}
+
+		for (int i = 0; i < UpdatedlocalParameterList.size(); i++) {
+			LocalParameter localparameter = UpdatedlocalParameterList.get(i);
+			String id = checkReservedKeywordPrism(localparameter.getId());
+			Double value = localparameter.getValue();
+			String name;
+			if (localparameter.getName() != null) {
+				name = localparameter.getName();
+			} else {
+				name = id;
+			}
+			out.write("const double " + id + " = " + value + "; // " + name + "\n"); // if not null name }
 
 		}
 
-		out.write("\n");
+		// System.err.println("Species Count: " + model.getSpeciesCount());
+		// System.err.println("Reaction Count: " + model.getReactionCount());
+
+		Map<String, String> map = new HashMap<String, String>();
+		for (int i = 0; i < reactionList.size(); i++) {
+			Reaction reaction = model.getReaction(i);
+			String SumReactant = "";
+			int reaStoch;
+			// System.err.println("Reaction: " + reaction);
+			// System.err.println("ReactantCount: " + reaction.getReactantCount());
+
+			for (int j = 0; j < reaction.getReactantCount(); j++) {
+				// System.err.println("Species: " + reaction.getReactant(j).getSpecies());
+				reaStoch = (int) reaction.getReactant(j).getStoichiometry() - 1;
+				// System.err.println("Stochiometry: " + reaStoch);
+				if (reaStoch == 0) {
+					SumReactant = SumReactant.concat(reaction.getReactant(j).getSpecies() + " >= " + reaStoch);
+				} else {
+					SumReactant = SumReactant.concat(reaction.getReactant(j).getSpecies() + " > " + reaStoch);
+				}
+
+				if (j < reaction.getReactantCount() - 1) {
+					SumReactant = SumReactant.concat(" & ");
+				}
+
+				// System.err.println(SumReactant);
+
+			}
+
+			map.put(reaction.getId(), SumReactant);
+
+			SumReactant = "";
+
+		}
+
+		// System.err.println(map);
+		// System.err.println(map.get("R0"));
 
 		// Identify model species
 		for (int i = 0; i < model.getSpeciesCount(); i++) {
 			// Write out syntax
 			// For function checkReservedKeywordPrism see below
 			Species species = model.getSpecies(i);
-			out.write("// Species " + checkReservedKeywordPrism(species.getId()) + "\n");
-			
+			String id = checkReservedKeywordPrism(species.getId());
+			int inAmount = (int) species.getInitialAmount();
+
+			out.write("\n");
+			out.write("// Species " + id + "\n");
+
 			if (unbound) {
-				out.write("// const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
-				out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
+				out.write("module " + id + "\n");
 				out.write("\n");
-				out.write("  // " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
-						+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
-						+ ";\n");
-				out.write("  " + checkReservedKeywordPrism(species.getId()) + "  :  " + "int init "
-						+ (int) (species.getInitialAmount()) + ";\n");
+				out.write("  " + id + "  :  " + "int init " + inAmount + ";\n");
 				out.write("\n");
 			} else {
-				out.write("const int " + checkReservedKeywordPrism(species.getId()) + "_MAX = MAX_AMOUNT;\n");
-				out.write("module " + checkReservedKeywordPrism(species.getId()) + "\n");
-				out.write("\n");
-				out.write("  " + checkReservedKeywordPrism(species.getId()) + " : " + "[0.."
-						+ checkReservedKeywordPrism(species.getId()) + "_MAX] init " + (int) species.getInitialAmount()
-						+ ";\n");
-				out.write("  // " + checkReservedKeywordPrism(species.getId()) + "  :  " + "int init "
-						+ (int) (species.getInitialAmount()) + ";\n");
-				out.write("\n");
+				System.err.println("Under Development");
+				/*
+				 * out.write("const int " + id + "_MAX = MAX_AMOUNT;\n"); out.write("module " +
+				 * id + "\n"); out.write("\n"); out.write("  " + id + " : " + "[0.." + id +
+				 * "_MAX] init " + inAmount + ";\n"); out.write("  // " + id + "  :  " +
+				 * "int init " + inAmount + ";\n"); out.write("\n");
+				 */
 			}
 
-			// Iterate over reactions
-			for (int j = 0; j < model.getReactionCount(); j++) {
-				Reaction reaction = model.getReaction(j);
-
+			for (int j = 0; j < reactionList.size(); j++) {
+				Reaction reaction = reactionList.get(j);
 				// Identify reactants and products
 				SpeciesReference reactant = reaction.getReactantForSpecies(species.getId());
 				SpeciesReference product = reaction.getProductForSpecies(species.getId());
+				String reactionId = checkReservedKeywordPrism(reaction.getId());
+				String speciesId = checkReservedKeywordPrism(species.getId());
+				int stochi;
 
-				if (reactant != null) {
-					out.write("		// " + checkReservedKeywordPrism(reaction.getId()) + "\n");
-					out.write("		[" + checkReservedKeywordPrism(reaction.getId()) + "] "
-							+ checkReservedKeywordPrism(species.getId()) + " > "
-							+ (int) (reactant.getStoichiometry() - 1) + " -> ("
-							+ checkReservedKeywordPrism(species.getId()) + "\'="
-							+ checkReservedKeywordPrism(species.getId()) + "-" + (int) reactant.getStoichiometry()
-							+ ");\n");
-				} else if (product != null) {
-					
-					if (unbound) {
-						out.write("		// " + checkReservedKeywordPrism(reaction.getId()) + "\n");
-						out.write("		[" + checkReservedKeywordPrism(reaction.getId()) + "] "
-								+ checkReservedKeywordPrism(species.getId()) + " >= " + "0 -> ("
-								+ checkReservedKeywordPrism(species.getId()) + "\'="
-								+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
-								+ ");\n");
+				if (reactant != null && product != null) {
+
+					int reaStoch = (int) reactant.getStoichiometry();
+					int proStoch = (int) product.getStoichiometry();
+					// System.err.println("Check 1");
+					stochi = proStoch - reaStoch;
+
+					out.write("		// " + reactionId + "\n");
+
+					if (stochi >= 0) {
+						out.write("		[" + reactionId + "] ");
+						if (map.get(reactionId) != null) {
+							out.write(map.get(reactionId));
+						}
+						out.write(" -> (" + speciesId + "\' = " + speciesId + " + " + stochi + ");\n");
 					} else {
-						out.write("		// " + checkReservedKeywordPrism(reaction.getId()) + "\n");
-						out.write("		[" + checkReservedKeywordPrism(reaction.getId()) + "] "
-								+ checkReservedKeywordPrism(species.getId()) + " <= " + checkReservedKeywordPrism(species.getId()) + "_MAX-" 
-								+ (int) product.getStoichiometry() + " -> ("
-								+ checkReservedKeywordPrism(species.getId()) + "\'="
-								+ checkReservedKeywordPrism(species.getId()) + "+" + (int) product.getStoichiometry()
-								+ ");\n");
-					}	
-					
+						out.write("		[" + reactionId + "] " + speciesId + " >  0 -> (" + speciesId + "\' = "
+								+ speciesId + " - " + Math.abs(stochi) + ");\n");
+					}
+
+				} else if (reactant == null && product != null) {
+
+					int proStoch = (int) product.getStoichiometry();
+					int reaStoch = 0;
+					// System.err.println("Check 2");
+					stochi = proStoch - reaStoch;
+
+					out.write("		// " + reactionId + "\n");
+					out.write("		[" + reactionId + "] ");
+
+					// System.err.println(reactionId);
+					// System.err.println(map.get(reactionId));
+					if (map.get(reactionId) != null && !"".equals(map.get(reactionId))) {
+						// System.err.println(map.get(reactionId) );
+						out.write(map.get(reactionId) + " -> (");
+					} else if ("".equals(map.get(reactionId))) {
+						out.write(speciesId + " >= 0 -> (");
+					}
+					out.write(speciesId + "\' = " + speciesId + " + " + stochi + ");\n");
+				} else if (reactant != null && product == null) {
+					int proStoch = 0;
+					int reaStoch = (int) reactant.getStoichiometry();
+					// System.err.println("Check 3");
+					stochi = proStoch - reaStoch;
+					out.write("		// " + reactionId + "\n");
+					out.write("		[" + reactionId + "] ");
+					if (map.get(reactionId) != null) {
+						out.write(map.get(reactionId));
+					}
+					out.write(" -> (" + speciesId + "\' = " + speciesId + " - " + Math.abs(stochi) + ");\n");
+				}
+			}
+
+			out.write("\n");
+			out.write("endmodule\n");
+		}
+
+		// Identify reaction rate
+		out.write("\n");
+		out.write("// Reaction rates\n");
+		out.write("module reaction_rates\n");
+		out.write("\n");
+
+		for (int i = 0; i < reactionList.size(); i++) {
+			Reaction reaction = reactionList.get(i);
+			String reactionId = checkReservedKeywordPrism(reaction.getId());
+
+			// Write state transitions
+			out.write("		// " + reactionId + ": ");
+
+			for (int j = 0; j < reaction.getReactantCount(); j++) {
+				if ((int) reaction.getReactant(j).getStoichiometry() > 1) {
+					out.write((int) reaction.getReactant(j).getStoichiometry() + " ");
+				}
+				// System.err.println(checkReservedKeywordPrism(reaction.getReactant(j).getSpecies()));
+				out.write(checkReservedKeywordPrism(reaction.getReactant(j).getSpecies()));
+				if (j < reaction.getReactantCount() - 1) {
+					out.write(" + ");
+				}
+			}
+			out.write(" -> ");
+
+			for (int j = 0; j < reaction.getProductCount(); j++) {
+				if ((int) reaction.getProduct(j).getStoichiometry() > 1) {
+					out.write((int) reaction.getProduct(j).getStoichiometry() + " ");
+				}
+				out.write(checkReservedKeywordPrism(reaction.getProduct(j).getSpecies()));
+				if (j < reaction.getProductCount() - 1) {
+					out.write(" + ");
 				}
 
 			}
 
 			out.write("\n");
-			out.write("endmodule\n");
-			out.write("\n");
 
-		}
+			String math = checkReserveKeywordMath(
+					SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model);
 
-		// Identify reaction rate
-		out.write("// Reaction rates\n");
-		out.write("module reaction_rates\n");
-		out.write("\n");
+			// System.err.println(math);
+			// System.err.println(localParameterList);
 
-		for (int i = 0; i < model.getReactionCount(); i++) {
-			Reaction reaction = model.getReaction(i);
-
-			// Write state transitions
-			out.write("		// " + checkReservedKeywordPrism(reaction.getId()) + ":  ->  ");
-			for (int j = 0; j < reaction.getProductCount(); j++) {
-				out.write(checkReservedKeywordPrism(reaction.getProduct(j).getSpecies()) + " ");
+			for (int l = 0; l < reaction.getKineticLaw().getLocalParameterCount(); l++) {
+				String locPara = reaction.getKineticLaw().getLocalParameter(l).getId();
+				math = math.replace(locPara.replace("local_", "").replace("_" + i, ""), locPara);
 			}
-			out.write("\n");
+
+			// System.err.println(math);
 
 			// Get the math for the reaction rate
-			out.write("		[" + checkReservedKeywordPrism(reaction.getId()) + "]  "
-					+ checkReserveKeywordMath(
-							SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model)
-					+ " > 0 -> " + "("
-					+ checkReserveKeywordMath(
-							SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model)
-					+ ") : true;\n");
+			out.write("		[" + reactionId + "] " + math + " > 0 -> " + math + " : true;\n");
 			out.write("\n");
-
 		}
+
 		out.write("endmodule\n");
 
-		out.write("\n");
-
 		// Identify rewards
+		out.write("\n");
 		out.write("// Reward structures (one per species)");
 		out.write("\n");
 
 		for (int i = 0; i < model.getSpeciesCount(); i++) {
 			Species species = model.getSpecies(i);
+			String speciesId = checkReservedKeywordPrism(species.getId().replace(" ", ""));
 
-			out.write("// Reward " + (i + 1) + ": " + checkReservedKeywordPrism(species.getId()) + "\n");
-			out.write("rewards " + "\"" + checkReservedKeywordPrism(species.getId()) + "\" true : "
-					+ checkReservedKeywordPrism(species.getId()) + "; endrewards\n");
+			out.write("// Reward " + (i + 1) + ": " + speciesId + "\n");
+			out.write("rewards " + "\"" + speciesId + "\" true : " + speciesId + "; endrewards\n");
 
 		}
 
 		out.close();
 
-		writePRISMProperty(filename, model);
+		// writePRISMProperty(filename, model);
 
 	}
 
-	
 	/*
-	 * Writes PRISM property Input: (String) filename, (Model) model
-	 * Output: void
+	 * Writes PRISM property Input: (String) filename, (Model) model Output: void
 	 * 
-	 * Function checks the constraints of a SBML model and translates it 
-	 * into the PRISM syntax. The properties are then written into a 
-	 * .props file.
+	 * Function checks the constraints of a SBML model and translates it into the
+	 * PRISM syntax. The properties are then written into a .props file.
 	 */
-	private static void writePRISMProperty(String filename, Model model) throws IOException
-	{
+	private static void writePRISMProperty(String filename, Model model) throws IOException {
 		// Write Properties File
 		File property = new File(filename.replace(".xml", ".props"));
 		FileWriter property_out = new FileWriter(property);
@@ -332,15 +508,20 @@ public class SBML2PRISM {
 			if (speciesString.contains(keywords.get(i))) {
 				// Replace species in math equations
 				// In equations species names are lead by a space
-				String Target = " " + keywords.get(i);
-				// System.err.println(Target);
-				math = math.replace(Target, "_" + keywords.get(i));
+				// String Target = " " + keywords.get(i);
+				// System.err.println("Target " + Target);
+				// System.err.println(math);
+				// math = math.replace("(?<!\\S)" + keywords.get(i) + "(?!\\S)", "_" +
+				// keywords.get(i));
+				math = math.replace(" " + keywords.get(i) + " ", " _" + keywords.get(i));
+				math = math.replace(" " + keywords.get(i) + ")", " _" + keywords.get(i) + ")");
+				math = math.replace("(" + keywords.get(i) + " ", "( _" + keywords.get(i));
 				// System.err.println(math);
 
 				// Replace species names in property files
 				// In property files species names are lead by a (
-				String TargetProperty = "(" + keywords.get(i);
-				math = math.replace(TargetProperty, "(_" + keywords.get(i));
+				// String TargetProperty = "(" + keywords.get(i);
+				// math = math.replace(TargetProperty, "(_" + keywords.get(i));
 			}
 
 		}
diff --git a/prismtest/Circuit0x8E/AmtRpart_module.xml b/prismtest/Circuit0x8E/AmtRpart_module.xml
new file mode 100644
index 000000000..b4a225e55
--- /dev/null
+++ b/prismtest/Circuit0x8E/AmtRpart_module.xml
@@ -0,0 +1,380 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="AmtRpart_module" metaid="iBioSim1">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell"/>
+      <comp:port comp:id="output__AmtR_protein" comp:idRef="AmtR_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__HlyIIR_protein" comp:idRef="HlyIIR_protein" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="input__Ara_AraC_protein" comp:idRef="Ara_AraC_protein" sboTerm="SBO:0000600"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="29" layout:width="99"/>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__pBAD" layout:species="pBAD">
+            <layout:boundingBox>
+              <layout:position layout:x="-1" layout:y="-1"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__pHlyIIR" layout:species="pHlyIIR">
+            <layout:boundingBox>
+              <layout:position layout:x="-1" layout:y="-1"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__pBAD" layout:id="TextGlyph__pBAD" layout:text="pBAD">
+            <layout:boundingBox>
+              <layout:position layout:x="-1" layout:y="-1"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__pHlyIIR" layout:id="TextGlyph__pHlyIIR" layout:text="pHlyIIR">
+            <layout:boundingBox>
+              <layout:position layout:x="-1" layout:y="-1"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="AmtR_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AmtR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AmtR_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="HlyIIR_protein" initialAmount="0" metaid="iBioSim3" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Ara_AraC_protein" initialAmount="0" metaid="iBioSim4" sboTerm="SBO:0000253">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pBAD" initialAmount="2" metaid="iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pHlyIIR" initialAmount="2" metaid="iBioSim6" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfReactions>
+      <reaction compartment="Cell" id="AmtR_protein_interaction_0" metaid="iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim9" species="AmtR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim9">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pBAD">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim8">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> pBAD </ci>
+                <apply>
+                  <plus/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> kb </ci>
+                      <apply>
+                        <divide/>
+                        <ci> ko_f </ci>
+                        <ci> ko_r </ci>
+                      </apply>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <times/>
+                        <ci> ka </ci>
+                        <apply>
+                          <divide/>
+                          <ci> kao_f </ci>
+                          <ci> kao_r </ci>
+                        </apply>
+                      </apply>
+                      <ci> nr </ci>
+                    </apply>
+                    <apply>
+                      <power/>
+                      <apply>
+                        <times/>
+                        <apply>
+                          <divide/>
+                          <ci> ka_f </ci>
+                          <ci> ka_r </ci>
+                        </apply>
+                        <ci> Ara_AraC_protein </ci>
+                      </apply>
+                      <ci> nc </ci>
+                    </apply>
+                  </apply>
+                </apply>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kao_f </ci>
+                      <ci> kao_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <ci> ka_f </ci>
+                        <ci> ka_r </ci>
+                      </apply>
+                      <ci> Ara_AraC_protein </ci>
+                    </apply>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="AmtR_protein_interaction_1" metaid="iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim12" species="AmtR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pHlyIIR">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pHlyIIR </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> HlyIIR_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/AraCsensor_module.xml b/prismtest/Circuit0x8E/AraCsensor_module.xml
new file mode 100644
index 000000000..947db0f31
--- /dev/null
+++ b/prismtest/Circuit0x8E/AraCsensor_module.xml
@@ -0,0 +1,41 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="AraCsensor_module" metaid="iBioSim1">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/AraCsensor_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell"/>
+      <comp:port comp:id="output__AraC_protein" comp:idRef="AraC_protein" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="0" layout:width="0"/>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="AraC_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AraC_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AraC_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AraCsensor/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/BetIpart_module.xml b/prismtest/Circuit0x8E/BetIpart_module.xml
new file mode 100644
index 000000000..c17495544
--- /dev/null
+++ b/prismtest/Circuit0x8E/BetIpart_module.xml
@@ -0,0 +1,464 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="BetIpart_module" metaid="iBioSim13">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__HlyIIR_protein" comp:idRef="HlyIIR_protein" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="output__BetI_protein" comp:idRef="BetI_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__TetR_protein" comp:idRef="TetR_protein" sboTerm="SBO:0000600"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__pHlyIIR" layout:species="pHlyIIR">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__pTet" layout:species="pTet">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__pHlyIIR__Production__BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pHlyIIR__Production__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__pHlyIIR">
+            <layout:boundingBox>
+              <layout:position layout:x="50" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__pHlyIIR" layout:role="product" layout:speciesGlyph="Glyph__pHlyIIR">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="20"/>
+                      <layout:end layout:x="50" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__pTet__Production__BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pTet__Production__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__pTet">
+            <layout:boundingBox>
+              <layout:position layout:x="180" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR_protein__repression__pTet" layout:role="product" layout:speciesGlyph="Glyph__pTet">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="20"/>
+                      <layout:end layout:x="180" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__pHlyIIR" layout:id="TextGlyph__pHlyIIR" layout:text="pHlyIIR">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__pTet" layout:id="TextGlyph__pTet" layout:text="pTet">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__HlyIIR_protein" layout:id="TextGlyph__HlyIIR_protein" layout:text="HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__BetI_protein" layout:id="TextGlyph__BetI_protein" layout:text="BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__TetR_protein" layout:id="TextGlyph__TetR_protein" layout:text="TetR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions/>
+    <listOfUnitDefinitions/>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="HlyIIR_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pHlyIIR" initialAmount="2" metaid="iBioSim3" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pTet" initialAmount="2" metaid="iBioSim4" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="BetI_protein" initialAmount="0" metaid="iBioSim5" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="TetR_protein" initialAmount="0" metaid="iBioSim6" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim27" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfConstraints/>
+    <listOfReactions>
+      <reaction compartment="Cell" id="BetI_protein_interaction_0" metaid="iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim9" species="BetI_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim9">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pHlyIIR">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim8">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pHlyIIR </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> HlyIIR_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="BetI_protein_interaction_1" metaid="iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim12" species="BetI_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pTet">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pTet </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> TetR_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents/>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/HlyIIRpart_module.xml b/prismtest/Circuit0x8E/HlyIIRpart_module.xml
new file mode 100644
index 000000000..fb3c18ffb
--- /dev/null
+++ b/prismtest/Circuit0x8E/HlyIIRpart_module.xml
@@ -0,0 +1,508 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="HlyIIRpart_module" metaid="iBioSim13">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__HlyIIR_protein" comp:idRef="HlyIIR_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__TetR_protein" comp:idRef="TetR_protein" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="input__Ara_AraC_protein" comp:idRef="Ara_AraC_protein" sboTerm="SBO:0000600"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__pTet" layout:species="pTet">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__pBAD" layout:species="pBAD">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="28" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__pTet__Production__HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pTet__Production__HlyIIR_protein" layout:role="product" layout:speciesGlyph="Glyph__HlyIIR_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__activation__pTet">
+            <layout:boundingBox>
+              <layout:position layout:x="180" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Ara_AraC_protein__activation__pTet" layout:role="product" layout:speciesGlyph="Glyph__pTet">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="20"/>
+                      <layout:end layout:x="180" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__pBAD__Production__HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pBAD__Production__HlyIIR_protein" layout:role="product" layout:speciesGlyph="Glyph__HlyIIR_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__pBAD">
+            <layout:boundingBox>
+              <layout:position layout:x="50" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR_protein__repression__pBAD" layout:role="product" layout:speciesGlyph="Glyph__pBAD">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="48" layout:y="20"/>
+                      <layout:end layout:x="50" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__pTet" layout:id="TextGlyph__pTet" layout:text="pTet">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__pBAD" layout:id="TextGlyph__pBAD" layout:text="pBAD">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__HlyIIR_protein" layout:id="TextGlyph__HlyIIR_protein" layout:text="HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__TetR_protein" layout:id="TextGlyph__TetR_protein" layout:text="TetR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="28" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Ara_AraC_protein" layout:id="TextGlyph__Ara_AraC_protein" layout:text="Ara_AraC_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions/>
+    <listOfUnitDefinitions/>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="HlyIIR_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="TetR_protein" initialAmount="0" metaid="iBioSim3" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pTet" initialAmount="2" metaid="iBioSim4" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pBAD" initialAmount="2" metaid="iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Ara_AraC_protein" initialAmount="0" metaid="iBioSim6" sboTerm="SBO:0000253">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim27" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfConstraints/>
+    <listOfReactions>
+      <reaction compartment="Cell" id="HlyIIR_protein_interaction_0" metaid="iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim9">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pTet">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim8">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> pTet </ci>
+                <apply>
+                  <plus/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> kb </ci>
+                      <apply>
+                        <divide/>
+                        <ci> ko_f </ci>
+                        <ci> ko_r </ci>
+                      </apply>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <times/>
+                        <ci> ka </ci>
+                        <apply>
+                          <divide/>
+                          <ci> kao_f </ci>
+                          <ci> kao_r </ci>
+                        </apply>
+                      </apply>
+                      <ci> nr </ci>
+                    </apply>
+                    <apply>
+                      <power/>
+                      <apply>
+                        <times/>
+                        <apply>
+                          <divide/>
+                          <ci> ka_f </ci>
+                          <ci> ka_r </ci>
+                        </apply>
+                        <ci> Ara_AraC_protein </ci>
+                      </apply>
+                      <ci> nc </ci>
+                    </apply>
+                  </apply>
+                </apply>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kao_f </ci>
+                      <ci> kao_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <ci> ka_f </ci>
+                        <ci> ka_r </ci>
+                      </apply>
+                      <ci> Ara_AraC_protein </ci>
+                    </apply>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="HlyIIR_protein_interaction_1" metaid="iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pBAD">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pBAD </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> TetR_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents/>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/LacIsensor_module.xml b/prismtest/Circuit0x8E/LacIsensor_module.xml
new file mode 100644
index 000000000..834a13b1c
--- /dev/null
+++ b/prismtest/Circuit0x8E/LacIsensor_module.xml
@@ -0,0 +1,41 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="LacIsensor_module" metaid="iBioSim1">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/LacIsensor_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell"/>
+      <comp:port comp:id="output__LacI_protein" comp:idRef="LacI_protein" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="0" layout:width="0"/>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="LacI_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/LacI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/LacI_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/LacIsensor/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/PhlFpart_module.xml b/prismtest/Circuit0x8E/PhlFpart_module.xml
new file mode 100644
index 000000000..8bdf95547
--- /dev/null
+++ b/prismtest/Circuit0x8E/PhlFpart_module.xml
@@ -0,0 +1,464 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="PhlFpart_module" metaid="iBioSim13">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__PhlF_protein" comp:idRef="PhlF_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__AmtR_protein" comp:idRef="AmtR_protein" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="input__LacI_protein" comp:idRef="LacI_protein" sboTerm="SBO:0000600"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__pTac" layout:species="pTac">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__pAmtR" layout:species="pAmtR">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__pTac__Production__PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pTac__Production__PhlF_protein" layout:role="product" layout:speciesGlyph="Glyph__PhlF_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__LacI_protein__repression__pTac">
+            <layout:boundingBox>
+              <layout:position layout:x="180" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI_protein__repression__pTac" layout:role="product" layout:speciesGlyph="Glyph__pTac">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="20"/>
+                      <layout:end layout:x="180" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__pAmtR__Production__PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pAmtR__Production__PhlF_protein" layout:role="product" layout:speciesGlyph="Glyph__PhlF_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__AmtR_protein__repression__pAmtR">
+            <layout:boundingBox>
+              <layout:position layout:x="50" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__AmtR_protein__repression__pAmtR" layout:role="product" layout:speciesGlyph="Glyph__pAmtR">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="20"/>
+                      <layout:end layout:x="50" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__pTac" layout:id="TextGlyph__pTac" layout:text="pTac">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__pAmtR" layout:id="TextGlyph__pAmtR" layout:text="pAmtR">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__PhlF_protein" layout:id="TextGlyph__PhlF_protein" layout:text="PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__AmtR_protein" layout:id="TextGlyph__AmtR_protein" layout:text="AmtR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__LacI_protein" layout:id="TextGlyph__LacI_protein" layout:text="LacI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions/>
+    <listOfUnitDefinitions/>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="PhlF_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="AmtR_protein" initialAmount="0" metaid="iBioSim3" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AmtR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AmtR_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="LacI_protein" initialAmount="0" metaid="iBioSim4" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/LacI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/LacI_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pTac" initialAmount="2" metaid="iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pAmtR" initialAmount="2" metaid="iBioSim6" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim27" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfConstraints/>
+    <listOfReactions>
+      <reaction compartment="Cell" id="PhlF_protein_interaction_0" metaid="iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim9" species="PhlF_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim9">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pTac">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim8">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pTac </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> LacI_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="PhlF_protein_interaction_1" metaid="iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim12" species="PhlF_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pAmtR">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pAmtR </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> AmtR_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents/>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/TetRsensor_module.xml b/prismtest/Circuit0x8E/TetRsensor_module.xml
new file mode 100644
index 000000000..b7828b22e
--- /dev/null
+++ b/prismtest/Circuit0x8E/TetRsensor_module.xml
@@ -0,0 +1,41 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="TetRsensor_module" metaid="iBioSim1">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/TetRsensor_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell"/>
+      <comp:port comp:id="output__TetR_protein" comp:idRef="TetR_protein" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="0" layout:width="0"/>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="TetR_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/TetRsensor/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/YFPpart_module.xml b/prismtest/Circuit0x8E/YFPpart_module.xml
new file mode 100644
index 000000000..2f853244a
--- /dev/null
+++ b/prismtest/Circuit0x8E/YFPpart_module.xml
@@ -0,0 +1,464 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="YFPpart_module" metaid="iBioSim13">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__YFP_protein" comp:idRef="YFP_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__BetI_protein" comp:idRef="BetI_protein" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="input__PhlF_protein" comp:idRef="PhlF_protein" sboTerm="SBO:0000600"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__pPhlF" layout:species="pPhlF">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__pBetI" layout:species="pBetI">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__pPhlF__Production__YFP_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pPhlF__Production__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__PhlF_protein__repression__pPhlF">
+            <layout:boundingBox>
+              <layout:position layout:x="180" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__PhlF_protein__repression__pPhlF" layout:role="product" layout:speciesGlyph="Glyph__pPhlF">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="20"/>
+                      <layout:end layout:x="180" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__pBetI__Production__YFP_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="115" layout:y="214.4775390625"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pBetI__Production__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="105"/>
+                      <layout:end layout:x="115" layout:y="214.4775390625"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__BetI_protein__repression__pBetI">
+            <layout:boundingBox>
+              <layout:position layout:x="50" layout:y="105"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__BetI_protein__repression__pBetI" layout:role="product" layout:speciesGlyph="Glyph__pBetI">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="20"/>
+                      <layout:end layout:x="50" layout:y="105"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__pPhlF" layout:id="TextGlyph__pPhlF" layout:text="pPhlF">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__pBetI" layout:id="TextGlyph__pBetI" layout:text="pBetI">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="90"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__YFP_protein" layout:id="TextGlyph__YFP_protein" layout:text="YFP_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="194.4775390625"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__BetI_protein" layout:id="TextGlyph__BetI_protein" layout:text="BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__PhlF_protein" layout:id="TextGlyph__PhlF_protein" layout:text="PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions/>
+    <listOfUnitDefinitions/>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="YFP_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="BetI_protein" initialAmount="0" metaid="iBioSim3" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pPhlF" initialAmount="2" metaid="iBioSim4" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pBetI" initialAmount="2" metaid="iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="PhlF_protein" initialAmount="0" metaid="iBioSim6" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim27" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfConstraints/>
+    <listOfReactions>
+      <reaction compartment="Cell" id="YFP_protein_interaction_0" metaid="iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim9" species="YFP_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim9">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pPhlF">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim8">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pPhlF </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> PhlF_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="YFP_protein_interaction_1" metaid="iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim12" species="YFP_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="pBetI">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> pBetI </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> BetI_protein </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents/>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E/manifest.xml b/prismtest/Circuit0x8E/manifest.xml
new file mode 100644
index 000000000..5175ad907
--- /dev/null
+++ b/prismtest/Circuit0x8E/manifest.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
+  <content location="." format="http://identifiers.org/combine.specifications/omex" />
+  <content location="./manifest.xml" format="http://identifiers.org/combine.specifications/omex-manifest" />
+  <content location="./topModelFlat.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./PhlFpart_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./LacIsensor_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./HlyIIRpart_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./TetRsensor_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./AraCsensor_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./Circuit0x8E_normal.sedml" format="http://identifiers.org/combine.specifications/sed-ml.level-1.version-2" master="true" />
+  <content location="./YFPpart_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./BetIpart_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./Circuit0x8E_normal.sbol" format="http://identifiers.org/combine.specifications/sbol.version-2" />
+  <content location="./topModel.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./AmtRpart_module.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" />
+</omexManifest>
diff --git a/prismtest/Circuit0x8E/results.txt b/prismtest/Circuit0x8E/results.txt
new file mode 100644
index 000000000..1543e6ca7
--- /dev/null
+++ b/prismtest/Circuit0x8E/results.txt
@@ -0,0 +1,2 @@
+0.0
+0.0010947156623888129
diff --git a/prismtest/Circuit0x8E/topModel.props b/prismtest/Circuit0x8E/topModel.props
new file mode 100644
index 000000000..2ead6d057
--- /dev/null
+++ b/prismtest/Circuit0x8E/topModel.props
@@ -0,0 +1,5 @@
+// File generated by SBML-to-PRISM converter
+// Original file: Circuit0x8E/topModel.xml
+// @GeneticLogicLab
+
+P=? [ true U[0,1000] (YFP_protein >= 30) ]
diff --git a/prismtest/Circuit0x8E/topModel.sm b/prismtest/Circuit0x8E/topModel.sm
new file mode 100644
index 000000000..6de0a8c1e
--- /dev/null
+++ b/prismtest/Circuit0x8E/topModel.sm
@@ -0,0 +1,518 @@
+// File generated by SBML-to-PRISM converter
+// Original file: Circuit0x8E/topModel.xml
+// @GeneticLogicLab
+
+ctmc
+
+ const int MAX_AMOUNT = 70;
+
+// Compartment size
+const double Cell = 1.0;
+
+// Model parameters
+const double kd = 0.0075; // Degradation rate
+const double kc_f = 0.05; // Forward complex formation rate
+const double kc_r = 1.0; // Reverse complex formation rate
+const double nc = 2.0; // Stoichiometry of binding
+const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
+const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
+const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
+const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
+const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
+const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
+const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
+const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
+const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
+const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
+const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
+const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
+const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
+const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
+const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
+const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
+const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
+const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
+const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
+const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
+const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
+const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
+const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
+const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
+const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
+const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
+const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
+const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
+const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
+const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
+const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
+const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
+const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
+const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
+const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
+const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
+const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
+const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
+const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
+const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
+const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
+const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
+const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
+const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
+const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
+const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
+const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
+const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
+const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
+const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
+const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
+const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
+const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
+const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
+const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
+const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
+const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
+const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
+const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
+const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
+const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
+const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
+const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
+const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
+const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
+const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
+const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
+const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
+const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
+const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
+const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
+const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
+const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
+const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
+const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
+
+// Species AmtR_protein
+const int AmtR_protein_MAX = MAX_AMOUNT;
+module AmtR_protein
+
+  AmtR_protein : [0..AmtR_protein_MAX] init 70;
+  // AmtR_protein  :  int init 70;
+
+		// AmtR_degradation_interaction
+		[AmtR_degradation_interaction] AmtR_protein > 0 -> (AmtR_protein'=AmtR_protein-1);
+		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
+		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
+		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
+		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
+
+endmodule
+
+// Species IPTG
+const int IPTG_MAX = MAX_AMOUNT;
+module IPTG
+
+  IPTG : [0..IPTG_MAX] init 0;
+  // IPTG  :  int init 0;
+
+		// Complex_IPTG_LacI_protein
+		[Complex_IPTG_LacI_protein] IPTG > 1 -> (IPTG'=IPTG-2);
+
+endmodule
+
+// Species Ara_AraC_protein
+const int Ara_AraC_protein_MAX = MAX_AMOUNT;
+module Ara_AraC_protein
+
+  Ara_AraC_protein : [0..Ara_AraC_protein_MAX] init 0;
+  // Ara_AraC_protein  :  int init 0;
+
+		// Ara_AraC_protein_degradation_interaction
+		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 0 -> (Ara_AraC_protein'=Ara_AraC_protein-1);
+		// Complex_Ara_AraC_protein
+		[Complex_Ara_AraC_protein] Ara_AraC_protein <= Ara_AraC_protein_MAX-1 -> (Ara_AraC_protein'=Ara_AraC_protein+1);
+
+endmodule
+
+// Species TetR_protein
+const int TetR_protein_MAX = MAX_AMOUNT;
+module TetR_protein
+
+  TetR_protein : [0..TetR_protein_MAX] init 0;
+  // TetR_protein  :  int init 0;
+
+		// Complex_aTc_TetR_protein
+		[Complex_aTc_TetR_protein] TetR_protein > 1 -> (TetR_protein'=TetR_protein-2);
+		// TetR_degradation_interaction
+		[TetR_degradation_interaction] TetR_protein > 0 -> (TetR_protein'=TetR_protein-1);
+
+endmodule
+
+// Species LacI_protein
+const int LacI_protein_MAX = MAX_AMOUNT;
+module LacI_protein
+
+  LacI_protein : [0..LacI_protein_MAX] init 0;
+  // LacI_protein  :  int init 0;
+
+		// Complex_IPTG_LacI_protein
+		[Complex_IPTG_LacI_protein] LacI_protein > 1 -> (LacI_protein'=LacI_protein-2);
+		// LacI_degradation_interaction
+		[LacI_degradation_interaction] LacI_protein > 0 -> (LacI_protein'=LacI_protein-1);
+
+endmodule
+
+// Species aTc_TetR_protein
+const int aTc_TetR_protein_MAX = MAX_AMOUNT;
+module aTc_TetR_protein
+
+  aTc_TetR_protein : [0..aTc_TetR_protein_MAX] init 0;
+  // aTc_TetR_protein  :  int init 0;
+
+		// Complex_aTc_TetR_protein
+		[Complex_aTc_TetR_protein] aTc_TetR_protein <= aTc_TetR_protein_MAX-1 -> (aTc_TetR_protein'=aTc_TetR_protein+1);
+		// aTc_TetR_protein_degradation_interaction
+		[aTc_TetR_protein_degradation_interaction] aTc_TetR_protein > 0 -> (aTc_TetR_protein'=aTc_TetR_protein-1);
+
+endmodule
+
+// Species AraC_protein
+const int AraC_protein_MAX = MAX_AMOUNT;
+module AraC_protein
+
+  AraC_protein : [0..AraC_protein_MAX] init 0;
+  // AraC_protein  :  int init 0;
+
+		// AraC_degradation_interaction
+		[AraC_degradation_interaction] AraC_protein > 0 -> (AraC_protein'=AraC_protein-1);
+		// Complex_Ara_AraC_protein
+		[Complex_Ara_AraC_protein] AraC_protein > 1 -> (AraC_protein'=AraC_protein-2);
+
+endmodule
+
+// Species IPTG_LacI_protein
+const int IPTG_LacI_protein_MAX = MAX_AMOUNT;
+module IPTG_LacI_protein
+
+  IPTG_LacI_protein : [0..IPTG_LacI_protein_MAX] init 0;
+  // IPTG_LacI_protein  :  int init 0;
+
+		// IPTG_LacI_protein_degradation_interaction
+		[IPTG_LacI_protein_degradation_interaction] IPTG_LacI_protein > 0 -> (IPTG_LacI_protein'=IPTG_LacI_protein-1);
+		// Complex_IPTG_LacI_protein
+		[Complex_IPTG_LacI_protein] IPTG_LacI_protein <= IPTG_LacI_protein_MAX-1 -> (IPTG_LacI_protein'=IPTG_LacI_protein+1);
+
+endmodule
+
+// Species aTc
+const int aTc_MAX = MAX_AMOUNT;
+module aTc
+
+  aTc : [0..aTc_MAX] init 0;
+  // aTc  :  int init 0;
+
+		// Complex_aTc_TetR_protein
+		[Complex_aTc_TetR_protein] aTc > 1 -> (aTc'=aTc-2);
+
+endmodule
+
+// Species BetI_protein
+const int BetI_protein_MAX = MAX_AMOUNT;
+module BetI_protein
+
+  BetI_protein : [0..BetI_protein_MAX] init 70;
+  // BetI_protein  :  int init 70;
+
+		// BetI_degradation_interaction
+		[BetI_degradation_interaction] BetI_protein > 0 -> (BetI_protein'=BetI_protein-1);
+		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
+		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
+		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
+		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
+
+endmodule
+
+// Species HlyIIR_protein
+const int HlyIIR_protein_MAX = MAX_AMOUNT;
+module HlyIIR_protein
+
+  HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0;
+  // HlyIIR_protein  :  int init 0;
+
+		// HlyIIR_degradation_interaction
+		[HlyIIR_degradation_interaction] HlyIIR_protein > 0 -> (HlyIIR_protein'=HlyIIR_protein-1);
+		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
+		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
+		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
+		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
+
+endmodule
+
+// Species PhlF_protein
+const int PhlF_protein_MAX = MAX_AMOUNT;
+module PhlF_protein
+
+  PhlF_protein : [0..PhlF_protein_MAX] init 70;
+  // PhlF_protein  :  int init 70;
+
+		// PhlF_degradation_interaction
+		[PhlF_degradation_interaction] PhlF_protein > 0 -> (PhlF_protein'=PhlF_protein-1);
+		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
+		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
+		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
+		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
+
+endmodule
+
+// Species YFP_protein
+const int YFP_protein_MAX = MAX_AMOUNT;
+module YFP_protein
+
+  YFP_protein : [0..YFP_protein_MAX] init 0;
+  // YFP_protein  :  int init 0;
+
+		// YFP_degradation_interaction
+		[YFP_degradation_interaction] YFP_protein > 0 -> (YFP_protein'=YFP_protein-1);
+		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
+		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
+		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
+		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
+
+endmodule
+
+// Species Ara
+const int Ara_MAX = MAX_AMOUNT;
+module Ara
+
+  Ara : [0..Ara_MAX] init 60;
+  // Ara  :  int init 60;
+
+		// Complex_Ara_AraC_protein
+		[Complex_Ara_AraC_protein] Ara > 1 -> (Ara'=Ara-2);
+
+endmodule
+
+// Species topModel_AmtRpart_module_sub__pBAD
+const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
+module topModel_AmtRpart_module_sub__pBAD
+
+  topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2;
+  // topModel_AmtRpart_module_sub__pBAD  :  int init 2;
+
+
+endmodule
+
+// Species topModel_AmtRpart_module_sub__pHlyIIR
+const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
+module topModel_AmtRpart_module_sub__pHlyIIR
+
+  topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2;
+  // topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
+
+
+endmodule
+
+// Species topModel_YFPpart_module_sub__pPhlF
+const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
+module topModel_YFPpart_module_sub__pPhlF
+
+  topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2;
+  // topModel_YFPpart_module_sub__pPhlF  :  int init 2;
+
+
+endmodule
+
+// Species topModel_YFPpart_module_sub__pBetI
+const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
+module topModel_YFPpart_module_sub__pBetI
+
+  topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2;
+  // topModel_YFPpart_module_sub__pBetI  :  int init 2;
+
+
+endmodule
+
+// Species topModel_BetIpart_module_sub__pHlyIIR
+const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
+module topModel_BetIpart_module_sub__pHlyIIR
+
+  topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2;
+  // topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
+
+
+endmodule
+
+// Species topModel_BetIpart_module_sub__pTet
+const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
+module topModel_BetIpart_module_sub__pTet
+
+  topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2;
+  // topModel_BetIpart_module_sub__pTet  :  int init 2;
+
+
+endmodule
+
+// Species topModel_PhlFpart_module_sub__pTac
+const int topModel_PhlFpart_module_sub__pTac_MAX = MAX_AMOUNT;
+module topModel_PhlFpart_module_sub__pTac
+
+  topModel_PhlFpart_module_sub__pTac : [0..topModel_PhlFpart_module_sub__pTac_MAX] init 2;
+  // topModel_PhlFpart_module_sub__pTac  :  int init 2;
+
+
+endmodule
+
+// Species topModel_PhlFpart_module_sub__pAmtR
+const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
+module topModel_PhlFpart_module_sub__pAmtR
+
+  topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2;
+  // topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
+
+
+endmodule
+
+// Species topModel_HlyIIRpart_module_sub__pTet
+const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
+module topModel_HlyIIRpart_module_sub__pTet
+
+  topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2;
+  // topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
+
+
+endmodule
+
+// Species topModel_HlyIIRpart_module_sub__pBAD
+const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
+module topModel_HlyIIRpart_module_sub__pBAD
+
+  topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2;
+  // topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
+
+
+endmodule
+
+// Reaction rates
+module reaction_rates
+
+		// AraC_degradation_interaction:  ->  
+		[AraC_degradation_interaction]  (kd * AraC_protein) > 0 -> ((kd * AraC_protein)) : true;
+
+		// Complex_aTc_TetR_protein:  ->  aTc_TetR_protein 
+		[Complex_aTc_TetR_protein]  (((kc_f * pow(TetR_protein , nc)) * pow(aTc , nc)) - (kc_r * aTc_TetR_protein)) > 0 -> ((((kc_f * pow(TetR_protein , nc)) * pow(aTc , nc)) - (kc_r * aTc_TetR_protein))) : true;
+
+		// TetR_degradation_interaction:  ->  
+		[TetR_degradation_interaction]  (kd * TetR_protein) > 0 -> ((kd * TetR_protein)) : true;
+
+		// Ara_AraC_protein_degradation_interaction:  ->  
+		[Ara_AraC_protein_degradation_interaction]  (kd * Ara_AraC_protein) > 0 -> ((kd * Ara_AraC_protein)) : true;
+
+		// IPTG_LacI_protein_degradation_interaction:  ->  
+		[IPTG_LacI_protein_degradation_interaction]  (kd * IPTG_LacI_protein) > 0 -> ((kd * IPTG_LacI_protein)) : true;
+
+		// PhlF_degradation_interaction:  ->  
+		[PhlF_degradation_interaction]  (kd * PhlF_protein) > 0 -> ((kd * PhlF_protein)) : true;
+
+		// aTc_TetR_protein_degradation_interaction:  ->  
+		[aTc_TetR_protein_degradation_interaction]  (kd * aTc_TetR_protein) > 0 -> ((kd * aTc_TetR_protein)) : true;
+
+		// Complex_IPTG_LacI_protein:  ->  IPTG_LacI_protein 
+		[Complex_IPTG_LacI_protein]  (((kc_f * pow(IPTG , nc)) * pow(LacI_protein , nc)) - (kc_r * IPTG_LacI_protein)) > 0 -> ((((kc_f * pow(IPTG , nc)) * pow(LacI_protein , nc)) - (kc_r * IPTG_LacI_protein))) : true;
+
+		// YFP_degradation_interaction:  ->  
+		[YFP_degradation_interaction]  (kd * YFP_protein) > 0 -> ((kd * YFP_protein)) : true;
+
+		// LacI_degradation_interaction:  ->  
+		[LacI_degradation_interaction]  (kd * LacI_protein) > 0 -> ((kd * LacI_protein)) : true;
+
+		// Complex_Ara_AraC_protein:  ->  Ara_AraC_protein 
+		[Complex_Ara_AraC_protein]  (((kc_f * pow(AraC_protein , nc)) * pow(Ara , nc)) - (kc_r * Ara_AraC_protein)) > 0 -> ((((kc_f * pow(AraC_protein , nc)) * pow(Ara , nc)) - (kc_r * Ara_AraC_protein))) : true;
+
+		// HlyIIR_degradation_interaction:  ->  
+		[HlyIIR_degradation_interaction]  (kd * HlyIIR_protein) > 0 -> ((kd * HlyIIR_protein)) : true;
+
+		// BetI_degradation_interaction:  ->  
+		[BetI_degradation_interaction]  (kd * BetI_protein) > 0 -> ((kd * BetI_protein)) : true;
+
+		// AmtR_degradation_interaction:  ->  
+		[AmtR_degradation_interaction]  (kd * AmtR_protein) > 0 -> ((kd * AmtR_protein)) : true;
+
+		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  ->  AmtR_protein 
+		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  ((topModel_AmtRpart_module_sub__pBAD * ((((topModel_AmtRpart_module_sub__kb * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) + ((((topModel_AmtRpart_module_sub__ka * topModel_AmtRpart_module_sub__kao_f) / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc)))) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + (((topModel_AmtRpart_module_sub__kao_f / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc)))) > 0 -> (((topModel_AmtRpart_module_sub__pBAD * ((((topModel_AmtRpart_module_sub__kb * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) + ((((topModel_AmtRpart_module_sub__ka * topModel_AmtRpart_module_sub__kao_f) / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc)))) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + (((topModel_AmtRpart_module_sub__kao_f / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc))))) : true;
+
+		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  ->  AmtR_protein 
+		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> ((((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc)))) : true;
+
+		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  ->  YFP_protein 
+		[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> ((((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc)))) : true;
+
+		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  ->  YFP_protein 
+		[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> ((((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc)))) : true;
+
+		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  ->  BetI_protein 
+		[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> ((((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc)))) : true;
+
+		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  ->  BetI_protein 
+		[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> ((((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc)))) : true;
+
+		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  ->  PhlF_protein 
+		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  (((((topModel_PhlFpart_module_sub__pTac * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * LacI_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> ((((((topModel_PhlFpart_module_sub__pTac * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * LacI_protein) , topModel_PhlFpart_module_sub__nc)))) : true;
+
+		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  ->  PhlF_protein 
+		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> ((((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc)))) : true;
+
+		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  ->  HlyIIR_protein 
+		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc))))) : true;
+
+		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  ->  HlyIIR_protein 
+		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> ((((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
+
+endmodule
+
+// Reward structures (one per species)
+// Reward 1: AmtR_protein
+rewards "AmtR_protein" true : AmtR_protein; endrewards
+// Reward 2: IPTG
+rewards "IPTG" true : IPTG; endrewards
+// Reward 3: Ara_AraC_protein
+rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
+// Reward 4: TetR_protein
+rewards "TetR_protein" true : TetR_protein; endrewards
+// Reward 5: LacI_protein
+rewards "LacI_protein" true : LacI_protein; endrewards
+// Reward 6: aTc_TetR_protein
+rewards "aTc_TetR_protein" true : aTc_TetR_protein; endrewards
+// Reward 7: AraC_protein
+rewards "AraC_protein" true : AraC_protein; endrewards
+// Reward 8: IPTG_LacI_protein
+rewards "IPTG_LacI_protein" true : IPTG_LacI_protein; endrewards
+// Reward 9: aTc
+rewards "aTc" true : aTc; endrewards
+// Reward 10: BetI_protein
+rewards "BetI_protein" true : BetI_protein; endrewards
+// Reward 11: HlyIIR_protein
+rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
+// Reward 12: PhlF_protein
+rewards "PhlF_protein" true : PhlF_protein; endrewards
+// Reward 13: YFP_protein
+rewards "YFP_protein" true : YFP_protein; endrewards
+// Reward 14: Ara
+rewards "Ara" true : Ara; endrewards
+// Reward 15: topModel_AmtRpart_module_sub__pBAD
+rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
+// Reward 16: topModel_AmtRpart_module_sub__pHlyIIR
+rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
+// Reward 17: topModel_YFPpart_module_sub__pPhlF
+rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
+// Reward 18: topModel_YFPpart_module_sub__pBetI
+rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
+// Reward 19: topModel_BetIpart_module_sub__pHlyIIR
+rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
+// Reward 20: topModel_BetIpart_module_sub__pTet
+rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
+// Reward 21: topModel_PhlFpart_module_sub__pTac
+rewards "topModel_PhlFpart_module_sub__pTac" true : topModel_PhlFpart_module_sub__pTac; endrewards
+// Reward 22: topModel_PhlFpart_module_sub__pAmtR
+rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
+// Reward 23: topModel_HlyIIRpart_module_sub__pTet
+rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
+// Reward 24: topModel_HlyIIRpart_module_sub__pBAD
+rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
diff --git a/prismtest/Circuit0x8E/topModel.xml b/prismtest/Circuit0x8E/topModel.xml
new file mode 100644
index 000000000..8485dba83
--- /dev/null
+++ b/prismtest/Circuit0x8E/topModel.xml
@@ -0,0 +1,1489 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <comp:listOfExternalModelDefinitions xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+    <comp:externalModelDefinition comp:id="AmtRpart_module" comp:md5="afa5a18689889291becde3bdbff34720" comp:source="AmtRpart_module.xml"/>
+    <comp:externalModelDefinition comp:id="AraCsensor_module" comp:md5="aea8373d33ed14e7c0d1ad9301f057c6" comp:source="AraCsensor_module.xml"/>
+    <comp:externalModelDefinition comp:id="YFPpart_module" comp:md5="17703319ea5f9084328f4079e6e512b5" comp:source="YFPpart_module.xml"/>
+    <comp:externalModelDefinition comp:id="TetRsensor_module" comp:md5="5233d3575ba60c37703789826e19a6f1" comp:source="TetRsensor_module.xml"/>
+    <comp:externalModelDefinition comp:id="BetIpart_module" comp:md5="98ce7971004a43fd7267d6ce346dbf9f" comp:source="BetIpart_module.xml"/>
+    <comp:externalModelDefinition comp:id="LacIsensor_module" comp:md5="d93c75be779f6d6d012d54aa4ed92fa2" comp:source="LacIsensor_module.xml"/>
+    <comp:externalModelDefinition comp:id="PhlFpart_module" comp:md5="2ff643eee1924804a82932e7426dce25" comp:source="PhlFpart_module.xml"/>
+    <comp:externalModelDefinition comp:id="HlyIIRpart_module" comp:md5="ed81d2f77d29e03f03e172aded9b2780" comp:source="HlyIIRpart_module.xml"/>
+  </comp:listOfExternalModelDefinitions>
+  <model id="topModel" metaid="iBioSim39">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <comp:listOfSubmodels xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:submodel comp:id="topModel_AmtRpart_module_sub" comp:modelRef="AmtRpart_module" metaid="iBioSim43">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim39">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+      <comp:submodel comp:id="topModel_AraCsensor_module_sub" comp:modelRef="AraCsensor_module" metaid="iBioSim45">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim43">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AraCsensor_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+      <comp:submodel comp:id="topModel_YFPpart_module_sub" comp:modelRef="YFPpart_module" metaid="iBioSim49">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim45">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+      <comp:submodel comp:id="topModel_TetRsensor_module_sub" comp:modelRef="TetRsensor_module" metaid="iBioSim51">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim49">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/TetRsensor_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+      <comp:submodel comp:id="topModel_BetIpart_module_sub" comp:modelRef="BetIpart_module" metaid="iBioSim55">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim51">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+      <comp:submodel comp:id="topModel_LacIsensor_module_sub" comp:modelRef="LacIsensor_module" metaid="iBioSim57">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim55">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/LacIsensor_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+      <comp:submodel comp:id="topModel_PhlFpart_module_sub" comp:modelRef="PhlFpart_module" metaid="iBioSim61">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim57">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+      <comp:submodel comp:id="topModel_HlyIIRpart_module_sub" comp:modelRef="HlyIIRpart_module" metaid="iBioSim65">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim61">
+                <mts:Modules>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/1"/></rdf:Bag></mts:Modules></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </comp:submodel>
+    </comp:listOfSubmodels>
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__AmtR_protein" comp:idRef="AmtR_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__IPTG" comp:idRef="IPTG" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="output__Ara_AraC_protein" comp:idRef="Ara_AraC_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__TetR_protein" comp:idRef="TetR_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__LacI_protein" comp:idRef="LacI_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__aTc_TetR_protein" comp:idRef="aTc_TetR_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__AraC_protein" comp:idRef="AraC_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__IPTG_LacI_protein" comp:idRef="IPTG_LacI_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__aTc" comp:idRef="aTc" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="output__BetI_protein" comp:idRef="BetI_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__HlyIIR_protein" comp:idRef="HlyIIR_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__PhlF_protein" comp:idRef="PhlF_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__YFP_protein" comp:idRef="YFP_protein" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__Ara" comp:idRef="Ara" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="AmtR_degradation_interaction" comp:idRef="AmtR_degradation_interaction" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="BetI_degradation_interaction" comp:idRef="BetI_degradation_interaction" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="PhlF_degradation_interaction" comp:idRef="PhlF_degradation_interaction" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="842.955078125" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__topModel_AmtRpart_module_sub" layout:reference="topModel_AmtRpart_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="165" layout:y="442.955078125"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+          <layout:generalGlyph layout:id="Glyph__topModel_AraCsensor_module_sub" layout:reference="topModel_AraCsensor_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="59" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+          <layout:generalGlyph layout:id="Glyph__topModel_YFPpart_module_sub" layout:reference="topModel_YFPpart_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="306" layout:y="802.955078125"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+          <layout:generalGlyph layout:id="Glyph__topModel_TetRsensor_module_sub" layout:reference="topModel_TetRsensor_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="507" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+          <layout:generalGlyph layout:id="Glyph__topModel_BetIpart_module_sub" layout:reference="topModel_BetIpart_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="405" layout:y="442.955078125"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+          <layout:generalGlyph layout:id="Glyph__topModel_LacIsensor_module_sub" layout:reference="topModel_LacIsensor_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="284" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+          <layout:generalGlyph layout:id="Glyph__topModel_PhlFpart_module_sub" layout:reference="topModel_PhlFpart_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="255" layout:y="622.955078125"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+          <layout:generalGlyph layout:id="Glyph__topModel_HlyIIRpart_module_sub" layout:reference="topModel_HlyIIRpart_module_sub">
+            <layout:boundingBox>
+              <layout:position layout:x="297" layout:y="262.955078125"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="50"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__IPTG" layout:species="IPTG">
+            <layout:boundingBox>
+              <layout:position layout:x="263" layout:y="100"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="96" layout:y="181.4775390625"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="506" layout:y="90"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="336" layout:y="90"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__aTc_TetR_protein" layout:species="aTc_TetR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="390" layout:y="181.4775390625"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__AraC_protein" layout:species="AraC_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="167" layout:y="90"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__IPTG_LacI_protein" layout:species="IPTG_LacI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="229" layout:y="181.4775390625"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__aTc" layout:species="aTc">
+            <layout:boundingBox>
+              <layout:position layout:x="429" layout:y="100"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="200" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="317" layout:y="352.955078125"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="240" layout:y="100"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
+            <layout:boundingBox>
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+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Ara" initialAmount="60" metaid="iBioSim15" sboTerm="SBO:0000247">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim15">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
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+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.0075"/>
+      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
+      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
+    </listOfParameters>
+    <listOfInitialAssignments/>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">        
+          <apply>
+            <lt/>
+            <ci> YFP_protein </ci>
+            <cn type="integer"> 30 </cn>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="AraC_degradation_interaction" metaid="iBioSim69" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AraC_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim16" species="AraC_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim16">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> AraC_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Complex_aTc_TetR_protein" metaid="iBioSim17" reversible="true" sboTerm="SBO:0000177">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim17">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/aTc_TetR_protein_complex_formation"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim19" species="TetR_protein" stoichiometry="2">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim19">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+          <speciesReference constant="true" metaid="iBioSim20" species="aTc" stoichiometry="2">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim20">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/aTc"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim18" species="aTc_TetR_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim18">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/aTc_TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <minus/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <ci> kc_f </ci>
+                  <apply>
+                    <power/>
+                    <ci> TetR_protein </ci>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <ci> aTc </ci>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+              <apply>
+                <times/>
+                <ci> kc_r </ci>
+                <ci> aTc_TetR_protein </ci>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim70" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim21" species="TetR_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim21">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> TetR_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim71" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim22" species="Ara_AraC_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim22">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> Ara_AraC_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="IPTG_LacI_protein_degradation_interaction" metaid="iBioSim72" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/IPTG_LacI_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim23" species="IPTG_LacI_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim23">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/IPTG_LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> IPTG_LacI_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim24">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> PhlF_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="aTc_TetR_protein_degradation_interaction" metaid="iBioSim74" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/aTc_TetR_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim25" species="aTc_TetR_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim25">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/aTc_TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> aTc_TetR_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Complex_IPTG_LacI_protein" metaid="iBioSim26" reversible="true" sboTerm="SBO:0000177">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim26">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/IPTG_LacI_protein_complex_formation"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim28" species="IPTG" stoichiometry="2">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim28">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/IPTG"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+          <speciesReference constant="true" metaid="iBioSim29" species="LacI_protein" stoichiometry="2">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim29">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim27" species="IPTG_LacI_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim27">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/IPTG_LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <minus/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <ci> kc_f </ci>
+                  <apply>
+                    <power/>
+                    <ci> IPTG </ci>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <ci> LacI_protein </ci>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+              <apply>
+                <times/>
+                <ci> kc_r </ci>
+                <ci> IPTG_LacI_protein </ci>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="1">
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+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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+                  <rdf:Description rdf:about="#iBioSim30">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> YFP_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="LacI_degradation_interaction" metaid="iBioSim76" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim31" species="LacI_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim31">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> LacI_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Complex_Ara_AraC_protein" metaid="iBioSim32" reversible="true" sboTerm="SBO:0000177">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim32">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_complex_formation"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim34" species="AraC_protein" stoichiometry="2">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim34">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+          <speciesReference constant="true" metaid="iBioSim35" species="Ara" stoichiometry="2">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim35">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference constant="true" metaid="iBioSim33" species="Ara_AraC_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim33">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <minus/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <ci> kc_f </ci>
+                  <apply>
+                    <power/>
+                    <ci> AraC_protein </ci>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <ci> Ara </ci>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+              <apply>
+                <times/>
+                <ci> kc_r </ci>
+                <ci> Ara_AraC_protein </ci>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim36">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> HlyIIR_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim37">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> BetI_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false" sboTerm="SBO:0000179">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="1">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim38">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> AmtR_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents/>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Circuit0x8E_010to100.xml b/prismtest/Circuit0x8E_010to100.xml
new file mode 100644
index 000000000..8ec591992
--- /dev/null
+++ b/prismtest/Circuit0x8E_010to100.xml
@@ -0,0 +1,2009 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="300"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+            <layout:listOfReferenceGlyphs>
+              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="159" layout:y="380"/>
+                      <layout:end layout:x="145" layout:y="320"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+            </layout:listOfReferenceGlyphs>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="180"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="38" layout:y="5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="187" layout:y="0"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="126" layout:y="180"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="227" layout:y="180"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="121" layout:y="90"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="95" layout:y="270"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="139" layout:y="360"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="30"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="115" layout:y="290"/>
+                      <layout:end layout:x="30" layout:y="40"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="60"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__YFP_degradation_interaction__substrate__YFP_protein" layout:role="substrate" layout:speciesGlyph="Glyph__YFP_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="159" layout:y="380"/>
+                      <layout:end layout:x="50" layout:y="70"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
+            <layout:boundingBox>
+              <layout:position layout:x="60" layout:y="90"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="141" layout:y="110"/>
+                      <layout:end layout:x="70" layout:y="100"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__BetI_degradation_interaction" layout:reaction="BetI_degradation_interaction">
+            <layout:boundingBox>
+              <layout:position layout:x="80" layout:y="120"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__BetI_degradation_interaction__substrate__BetI_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BetI_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="247" layout:y="200"/>
+                      <layout:end layout:x="90" layout:y="130"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
+            <layout:boundingBox>
+              <layout:position layout:x="100" layout:y="150"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="40" layout:y="200"/>
+                      <layout:end layout:x="110" layout:y="160"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__repression__AmtR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="200"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Ara_AraC_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="88" layout:y="20"/>
+                      <layout:end layout:x="40" layout:y="200"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__AmtR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="200"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="141" layout:y="110"/>
+                      <layout:end layout:x="40" layout:y="200"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__PhlF_protein__repression__YFP_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="159" layout:y="380"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__PhlF_protein__repression__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="115" layout:y="290"/>
+                      <layout:end layout:x="159" layout:y="380"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__BetI_protein__repression__YFP_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="159" layout:y="380"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
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+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pBetI" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim3" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pTet" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
+      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
+      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <lt/>
+            <ci> YFP_protein </ci>
+            <cn type="integer"> 30 </cn>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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+          </math>
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+      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
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+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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+        </annotation>
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+          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
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+            </annotation>
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+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                </apply>
+                <ci> topModel_PhlFpart_module_sub__nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__kr_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__kr_r </ci>
+                    </apply>
+                    <ci> LacI_protein </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                </apply>
+                <ci> topModel_PhlFpart_module_sub__nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__kr_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__kr_r </ci>
+                    </apply>
+                    <ci> AmtR_protein </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim9">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim8">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> topModel_HlyIIRpart_module_sub__pTet </ci>
+                <apply>
+                  <plus/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <apply>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__kb </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                      </apply>
+                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
+                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                  </apply>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <apply>
+                          <times/>
+                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                        </apply>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                      </apply>
+                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    </apply>
+                    <apply>
+                      <power/>
+                      <apply>
+                        <times/>
+                        <apply>
+                          <divide/>
+                          <ci> topModel_HlyIIRpart_module_sub__ka_f </ci>
+                          <ci> topModel_HlyIIRpart_module_sub__ka_r </ci>
+                        </apply>
+                        <ci> Ara_AraC_protein </ci>
+                      </apply>
+                      <ci> topModel_HlyIIRpart_module_sub__nc </ci>
+                    </apply>
+                  </apply>
+                </apply>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
+                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                  </apply>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka_f </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__ka_r </ci>
+                      </apply>
+                      <ci> Ara_AraC_protein </ci>
+                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nc </ci>
+                  </apply>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
+                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                  </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
+                </apply>
+                <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
+                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_HlyIIRpart_module_sub__kr_f </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kr_r </ci>
+                    </apply>
+                    <ci> TetR_protein </ci>
+                  </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/prismtest/Circuit0x8E_LHF_010to100.xml b/prismtest/Circuit0x8E_LHF_010to100.xml
new file mode 100644
index 000000000..c1e2259fe
--- /dev/null
+++ b/prismtest/Circuit0x8E_LHF_010to100.xml
@@ -0,0 +1,2103 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+    <annotation>
+      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+          <rdf:Description rdf:about="#iBioSim1">
+            <mts:ModuleDefinitions>
+              <rdf:Bag>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+    </annotation>
+      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="50"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+            <layout:listOfReferenceGlyphs>
+              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="281" layout:y="380"/>
+                      <layout:end layout:x="45" layout:y="70"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+            </layout:listOfReferenceGlyphs>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
+            <layout:boundingBox>
+              <layout:position layout:x="370" layout:y="190"/>
+              <layout:dimensions layout:height="40" layout:width="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
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+          <layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="50"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="HlyIIR_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="LacI_protein" initialAmount="0" metaid="iBioSim5" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/LacI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/LacI_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Ara_AraC_protein" initialAmount="0" metaid="iBioSim6">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="BetI_protein" initialAmount="130" metaid="iBioSim7" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="PhlF_protein" initialAmount="70" metaid="iBioSim9" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim9">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="AmtR_protein" initialAmount="0" metaid="iBioSim10" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AmtR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AmtR_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="TetR_protein" initialAmount="60" metaid="iBioSim12" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim12">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="YFP_protein" initialAmount="0" metaid="iBioSim13" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim13">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="BM3R1_protein" initialAmount="70" metaid="iBioSim16" sboTerm="SBO:0000252">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim16">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BM3R1_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BM3R1_protein/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim3" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim4">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
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+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_AmtRpart_module_sub__pBM3R1" initialAmount="2" metaid="topModel_AmtRpart_module_sub__iBioSim2" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim2">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_AmtRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_AmtRpart_module_sub__iBioSim3" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter2_module_sub__Inverter2_fc" initialAmount="2" metaid="topModel_Inverter2_module_sub__iBioSim3" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pBetI" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pPhlF" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
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+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim3">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim5">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim6">
+                <mts:ComponentDefinitions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                  <rdf:Seq>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+            </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
+      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
+      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <lt/>
+            <ci> YFP_protein </ci>
+            <cn type="integer"> 30 </cn>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim25">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> BM3R1_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim26">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> PhlF_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim32">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> YFP_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim38">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> HlyIIR_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> BetI_protein </ci>
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+                <mts:Interactions>
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+        </annotation>
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+          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
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+          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
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+      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim7">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim9">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim8">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                </apply>
+                <ci> topModel_PhlFpart_module_sub__nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__kr_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__kr_r </ci>
+                    </apply>
+                    <ci> LacI_protein </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#iBioSim10">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfProducts>
+          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim12">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim11">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </modifierSpeciesReference>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                </apply>
+                <ci> topModel_PhlFpart_module_sub__nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
+                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> topModel_PhlFpart_module_sub__kr_f </ci>
+                      <ci> topModel_PhlFpart_module_sub__kr_r </ci>
+                    </apply>
+                    <ci> AmtR_protein </ci>
+                  </apply>
+                  <ci> topModel_PhlFpart_module_sub__nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        <annotation>
+          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+              <rdf:Description rdf:about="#">
+                <mts:Interactions>
+                  <rdf:Bag>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+        </annotation>
+              <listOfReactants>
+          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+            <annotation>
+              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
+                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
+                  <rdf:Description rdf:about="#iBioSim40">
+                    <mts:Participations>
+                      <rdf:Bag>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+            </annotation>
+                    </speciesReference>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> AmtR_protein </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/prismtest/Majority_10_10.xml b/prismtest/Majority_10_10.xml
new file mode 100644
index 000000000..cc64d5775
--- /dev/null
+++ b/prismtest/Majority_10_10.xml
@@ -0,0 +1,1427 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="2" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="Majority" metaid="iBioSim48">
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__A" comp:idRef="A" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="input__B" comp:idRef="B" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="reaction__Degradation_C" comp:idRef="Degradation_C" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__C" comp:idRef="C" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
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+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
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+            </layout:boundingBox>
+            <layout:listOfReferenceGlyphs>
+              <layout:referenceGlyph layout:glyph="Glyph__C" layout:id="Glyph__c0__substrate__C" layout:role="substrate">
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+                      <layout:start layout:x="760" layout:y="375"/>
+                      <layout:end layout:x="805" layout:y="260"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+              <layout:referenceGlyph layout:glyph="Glyph__E" layout:id="Glyph__c0__substrate__E" layout:role="substrate">
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+                      <layout:end layout:x="805" layout:y="260"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+            </layout:listOfReferenceGlyphs>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="10" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__A" layout:species="A">
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+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__X" layout:species="X">
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+              <layout:position layout:x="30" layout:y="320.5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
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+          <layout:speciesGlyph layout:id="Glyph__Y" layout:species="Y">
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+              <layout:dimensions layout:height="30" layout:width="100"/>
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+          <layout:speciesGlyph layout:id="Glyph__D" layout:species="D">
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+          <layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
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+          <layout:speciesGlyph layout:id="Glyph__Z" layout:species="Z">
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+          <layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
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+              <layout:dimensions layout:height="30" layout:width="100"/>
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+          <layout:textGlyph layout:graphicalObject="Glyph__P1" layout:id="TextGlyph__P1" layout:text="P1">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="130.5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P2" layout:id="TextGlyph__P2" layout:text="P2">
+            <layout:boundingBox>
+              <layout:position layout:x="220" layout:y="250"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P3" layout:id="TextGlyph__P3" layout:text="P3">
+            <layout:boundingBox>
+              <layout:position layout:x="410" layout:y="280.5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P4" layout:id="TextGlyph__P4" layout:text="P4">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="390.5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P5" layout:id="TextGlyph__P5" layout:text="P5">
+            <layout:boundingBox>
+              <layout:position layout:x="569.866721808" layout:y="70.47526385545098"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P6" layout:id="TextGlyph__P6" layout:text="P6">
+            <layout:boundingBox>
+              <layout:position layout:x="569.7472982594733" layout:y="20.21077559250824"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P7" layout:id="TextGlyph__P7" layout:text="P7">
+            <layout:boundingBox>
+              <layout:position layout:x="570" layout:y="210.5"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="780" layout:y="240"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_C" layout:id="TextGlyph__Degradation_C" layout:text="Degradation_C">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="30"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_D" layout:id="TextGlyph__Degradation_D" layout:text="Degradation_D">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="60"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_E" layout:id="TextGlyph__Degradation_E" layout:text="Degradation_E">
+            <layout:boundingBox>
+              <layout:position layout:x="60" layout:y="90"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_X" layout:id="TextGlyph__Degradation_X" layout:text="Degradation_X">
+            <layout:boundingBox>
+              <layout:position layout:x="80" layout:y="120"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_Y" layout:id="TextGlyph__Degradation_Y" layout:text="Degradation_Y">
+            <layout:boundingBox>
+              <layout:position layout:x="100" layout:y="150"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_Z" layout:id="TextGlyph__Degradation_Z" layout:text="Degradation_Z">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="180"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions>
+      <functionDefinition id="F" name="Eventually Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> t </ci>
+            </bvar>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <or/>
+              <apply>
+                <not/>
+                <ci> t </ci>
+              </apply>
+              <apply>
+                <not/>
+                <ci> x </ci>
+              </apply>
+            </apply>
+          </lambda>
+        </math>
+            </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="A" initialAmount="0" metaid="iBioSim1"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="X" initialAmount="70" metaid="iBioSim3"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Y" initialAmount="70" metaid="iBioSim5"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="D" initialAmount="70" metaid="iBioSim6"/>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="B" initialAmount="120" metaid="iBioSim7"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Z" initialAmount="0" metaid="iBioSim8"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="E" initialAmount="0" metaid="iBioSim9"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="C" initialAmount="70" metaid="iBioSim10"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P8" initialAmount="2" metaid="iBioSim11" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P1" initialAmount="2" metaid="iBioSim13" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P2" initialAmount="2" metaid="iBioSim15" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P3" initialAmount="2" metaid="iBioSim17" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P4" initialAmount="2" metaid="iBioSim19" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P5" initialAmount="2" metaid="iBioSim21" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P6" initialAmount="2" metaid="iBioSim23" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P7" initialAmount="2" metaid="iBioSim25" sboTerm="SBO:0000590"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim4" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim12" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim27" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim29" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim30" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim31" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim32" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim33" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim34" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim35" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim36" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim37" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim38" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim39" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim40" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="kd" metaid="iBioSim2" name="Degradation rate" value="0.00075"/>
+    </listOfParameters>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <ci> F </ci>
+            <apply>
+              <leq/>
+              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+              <cn type="integer"> 2100 </cn>
+            </apply>
+            <apply>
+              <and/>
+              <apply>
+                <gt/>
+                <ci> E </ci>
+                <cn type="integer"> 40 </cn>
+              </apply>
+              <apply>
+                <lt/>
+                <ci> C </ci>
+                <cn type="integer"> 20 </cn>
+              </apply>
+            </apply>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="Degradation_C" metaid="iBioSim46" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="C" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> C </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_D" metaid="iBioSim44" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="D" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> D </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_E" metaid="iBioSim45" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="E" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> E </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_X" metaid="iBioSim47" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> X </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_Y" metaid="iBioSim43" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> Y </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_Z" metaid="iBioSim42" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> Z </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P1" metaid="iBioSim14" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P1 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> A </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P2" metaid="iBioSim16" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P2 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> B </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P3" metaid="iBioSim18" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P3 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> D </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P4" metaid="iBioSim20" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="D" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P4 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> X </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P5" metaid="iBioSim22" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="D" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P5 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> Y </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P6" metaid="iBioSim24" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="D" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P6 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> Z </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P7" metaid="iBioSim26" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="E" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P7 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> D </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P8" metaid="iBioSim28" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="C" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="E"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P8 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> E </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/prismtest/SimpleChem.props b/prismtest/SimpleChem.props
new file mode 100644
index 000000000..3cf2a0d0e
--- /dev/null
+++ b/prismtest/SimpleChem.props
@@ -0,0 +1,5 @@
+// File generated by SBML-to-PRISM converter
+// Original file: SimpleChem.xml
+// @GeneticLogicLab
+
+P=? [F<=100 (S2 > 8)]
\ No newline at end of file
diff --git a/prismtest/SimpleChem.sm b/prismtest/SimpleChem.sm
new file mode 100644
index 000000000..5b2a5960b
--- /dev/null
+++ b/prismtest/SimpleChem.sm
@@ -0,0 +1,65 @@
+// File generated by SBML-to-PRISM converter
+// Original file: SimpleChem.xml
+// @GeneticLogicLab
+
+ctmc
+
+// const int MAX_AMOUNT = ADD VALUE 
+
+// Compartment size
+const double Cell = 1.0;
+
+// Model parameters
+const double kd = 0.0075; // Degradation rate
+
+// Species S0
+// const int S0_MAX = MAX_AMOUNT;
+module S0
+
+  // S0 : [0..S0_MAX] init 10;
+  S0  :  int init 10;
+
+		// R0
+		[R0] S0 > 0 -> (S0'=S0-1);
+
+endmodule
+
+// Species S1
+// const int S1_MAX = MAX_AMOUNT;
+module S1
+
+  // S1 : [0..S1_MAX] init 10;
+  S1  :  int init 10;
+
+		// R0
+		[R0] S1 > 0 -> (S1'=S1-1);
+
+endmodule
+
+// Species S2
+// const int S2_MAX = MAX_AMOUNT;
+module S2
+
+  // S2 : [0..S2_MAX] init 0;
+  S2  :  int init 0;
+
+		// R0
+		[R0] S2 >= 0 -> (S2'=S2+1);
+
+endmodule
+
+// Reaction rates
+module reaction_rates
+
+		// R0:  ->  S2 
+		[R0]  ((kf * S0) * S1) > 0 -> (((kf * S0) * S1)) : true;
+
+endmodule
+
+// Reward structures (one per species)
+// Reward 1: S0
+rewards "S0" true : S0; endrewards
+// Reward 2: S1
+rewards "S1" true : S1; endrewards
+// Reward 3: S2
+rewards "S2" true : S2; endrewards
diff --git a/prismtest/SimpleChem.xml b/prismtest/SimpleChem.xml
new file mode 100644
index 000000000..5d27c5bd8
--- /dev/null
+++ b/prismtest/SimpleChem.xml
@@ -0,0 +1,222 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="SimpleChem" metaid="iBioSim6">
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="657" layout:y="179"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+            <layout:listOfReferenceGlyphs>
+              <layout:referenceGlyph layout:glyph="Glyph__S2" layout:id="Glyph__c0__substrate__S2" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="480" layout:y="175"/>
+                      <layout:end layout:x="682" layout:y="199"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+            </layout:listOfReferenceGlyphs>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__S0" layout:species="S0">
+            <layout:boundingBox>
+              <layout:position layout:x="104" layout:y="93"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S1" layout:species="S1">
+            <layout:boundingBox>
+              <layout:position layout:x="128" layout:y="248"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S2" layout:species="S2">
+            <layout:boundingBox>
+              <layout:position layout:x="430" layout:y="160"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__R0" layout:reaction="R0">
+            <layout:boundingBox>
+              <layout:position layout:x="306" layout:y="178"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__R0__substrate__S0" layout:role="substrate" layout:speciesGlyph="Glyph__S0">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="154" layout:y="108"/>
+                      <layout:end layout:x="316" layout:y="188"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+              <layout:speciesReferenceGlyph layout:id="Glyph__R0__substrate__S1" layout:role="substrate" layout:speciesGlyph="Glyph__S1">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="178" layout:y="263"/>
+                      <layout:end layout:x="316" layout:y="188"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+              <layout:speciesReferenceGlyph layout:id="Glyph__R0__product__S2" layout:role="product" layout:speciesGlyph="Glyph__S2">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="316" layout:y="188"/>
+                      <layout:end layout:x="480" layout:y="175"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__S0" layout:id="TextGlyph__S0" layout:text="S0">
+            <layout:boundingBox>
+              <layout:position layout:x="104" layout:y="93"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__S1" layout:id="TextGlyph__S1" layout:text="S1">
+            <layout:boundingBox>
+              <layout:position layout:x="128" layout:y="248"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__R0" layout:id="TextGlyph__R0" layout:text="R0">
+            <layout:boundingBox>
+              <layout:position layout:x="306" layout:y="178"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__S2" layout:id="TextGlyph__S2" layout:text="S2">
+            <layout:boundingBox>
+              <layout:position layout:x="430" layout:y="160"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="657" layout:y="179"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions>
+      <functionDefinition id="F" name="Eventually Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">        
+          <lambda>
+            <bvar>
+              <ci> t </ci>
+            </bvar>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <or/>
+              <apply>
+                <not/>
+                <ci> t </ci>
+              </apply>
+              <apply>
+                <not/>
+                <ci> x </ci>
+              </apply>
+            </apply>
+          </lambda>
+        </math>
+            </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S0" initialAmount="10" metaid="iBioSim1"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S1" initialAmount="10" metaid="iBioSim3"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S2" initialAmount="0" metaid="iBioSim5"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kd" metaid="iBioSim2" name="Degradation rate" value="0.0075"/>
+    </listOfParameters>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">        
+          <apply>
+            <ci> F </ci>
+            <apply>
+              <leq/>
+              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+              <cn type="integer"> 100 </cn>
+            </apply>
+            <apply>
+              <gt/>
+              <ci> S2 </ci>
+              <cn type="integer"> 8 </cn>
+            </apply>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="R0" metaid="iBioSim4" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="S0" stoichiometry="1"/>
+          <speciesReference constant="true" species="S1" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference constant="true" species="S2" stoichiometry="1"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <apply>
+                <times/>
+                <ci> kf </ci>
+                <ci> S0 </ci>
+              </apply>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+                  <listOfLocalParameters>
+            <localParameter id="kf" value="0.1"/>
+            <localParameter id="kr" value="1"/>
+          </listOfLocalParameters>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/SimpleHierchyModel/DSensor.xml b/prismtest/SimpleHierchyModel/DSensor.xml
new file mode 100644
index 000000000..b20f60271
--- /dev/null
+++ b/prismtest/SimpleHierchyModel/DSensor.xml
@@ -0,0 +1,263 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="DSensor" metaid="iBioSim6">
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__S1" comp:idRef="S1" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="Degradation_S1" comp:idRef="Degradation_S1" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__D" comp:idRef="D" sboTerm="SBO:0000600"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__D" layout:species="D">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="127"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S1" layout:species="S1">
+            <layout:boundingBox>
+              <layout:position layout:x="490" layout:y="130"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P0" layout:species="P0">
+            <layout:boundingBox>
+              <layout:position layout:x="303" layout:y="151"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__P0__Production__S1">
+            <layout:boundingBox>
+              <layout:position layout:x="540" layout:y="145"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P0__Production__S1" layout:role="product" layout:speciesGlyph="Glyph__S1">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="353" layout:y="166"/>
+                      <layout:end layout:x="540" layout:y="145"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__D__activation__P0">
+            <layout:boundingBox>
+              <layout:position layout:x="353" layout:y="166"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__D__activation__P0" layout:role="product" layout:speciesGlyph="Glyph__P0">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="170" layout:y="142"/>
+                      <layout:end layout:x="353" layout:y="166"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__D" layout:id="TextGlyph__D" layout:text="D">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="127"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__S1" layout:id="TextGlyph__S1" layout:text="S1">
+            <layout:boundingBox>
+              <layout:position layout:x="490" layout:y="130"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P0" layout:id="TextGlyph__P0" layout:text="P0">
+            <layout:boundingBox>
+              <layout:position layout:x="303" layout:y="151"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions/>
+    <listOfUnitDefinitions/>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="D" initialAmount="60" metaid="iBioSim1"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S1" initialAmount="0" metaid="iBioSim3"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P0" initialAmount="2" metaid="iBioSim4" sboTerm="SBO:0000590"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim2" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim7" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim8" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim9" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim10" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim11" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim12" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim13" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim14" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim15" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim16" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim17" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim18" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim19" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim20" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="kd" metaid="iBioSim21" name="Degradation rate" value="0.0075"/>
+    </listOfParameters>
+    <listOfInitialAssignments/>
+    <listOfConstraints/>
+    <listOfReactions>
+      <reaction compartment="Cell" id="Production_P0" metaid="iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        <listOfReactants/>
+        <listOfProducts>
+          <speciesReference constant="true" species="S1" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P0"/>
+          <modifierSpeciesReference sboTerm="SBO:0000459" species="D"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> P0 </ci>
+                <apply>
+                  <plus/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <apply>
+                        <times/>
+                        <ci> kb </ci>
+                        <ci> ko_f </ci>
+                      </apply>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <apply>
+                          <times/>
+                          <ci> ka </ci>
+                          <ci> kao_f </ci>
+                        </apply>
+                        <ci> kao_r </ci>
+                      </apply>
+                      <ci> nr </ci>
+                    </apply>
+                    <apply>
+                      <power/>
+                      <apply>
+                        <times/>
+                        <apply>
+                          <divide/>
+                          <ci> ka_f </ci>
+                          <ci> ka_r </ci>
+                        </apply>
+                        <ci> D </ci>
+                      </apply>
+                      <ci> nc </ci>
+                    </apply>
+                  </apply>
+                </apply>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kao_f </ci>
+                      <ci> kao_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <ci> ka_f </ci>
+                        <ci> ka_r </ci>
+                      </apply>
+                      <ci> D </ci>
+                    </apply>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                  <listOfLocalParameters/>
+        </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_S1" metaid="iBioSim22" reversible="false" sboTerm="SBO:0000179">
+        <listOfReactants>
+          <speciesReference constant="true" species="S1" stoichiometry="1"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents/>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/SimpleHierchyModel/manifest.xml b/prismtest/SimpleHierchyModel/manifest.xml
new file mode 100644
index 000000000..c6a6be97e
--- /dev/null
+++ b/prismtest/SimpleHierchyModel/manifest.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<omexManifest xmlns="http://identifiers.org/combine.specifications/omex-manifest">
+  <content location="." format="http://identifiers.org/combine.specifications/omex" />
+  <content location="./manifest.xml" format="http://identifiers.org/combine.specifications/omex-manifest" />
+  <content location="./SimpleHierachyModel.sbol" format="http://identifiers.org/combine.specifications/sbol.version-2" />
+  <content location="./DSensor.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./SimpleHierachyModel.sedml" format="http://identifiers.org/combine.specifications/sed-ml.level-1.version-2" master="true" />
+  <content location="./topModel.xml" format="http://identifiers.org/combine.specifications/sbml.level-3.version-2.core" />
+  <content location="./metadata.rdf" format="http://identifiers.org/combine.specifications/omex-metadata" />
+</omexManifest>
diff --git a/prismtest/SimpleHierchyModel/metadata.rdf b/prismtest/SimpleHierchyModel/metadata.rdf
new file mode 100644
index 000000000..218b0511f
--- /dev/null
+++ b/prismtest/SimpleHierchyModel/metadata.rdf
@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2006/vcard/ns#" />
diff --git a/prismtest/SimpleHierchyModel/topModel.props b/prismtest/SimpleHierchyModel/topModel.props
new file mode 100644
index 000000000..699e82d3e
--- /dev/null
+++ b/prismtest/SimpleHierchyModel/topModel.props
@@ -0,0 +1,4 @@
+// File generated by SBML-to-PRISM converter
+// Original file: SimpleHierchyModel/topModel.xml
+// @GeneticLogicLab
+
diff --git a/prismtest/SimpleHierchyModel/topModel.sm b/prismtest/SimpleHierchyModel/topModel.sm
new file mode 100644
index 000000000..75e042b33
--- /dev/null
+++ b/prismtest/SimpleHierchyModel/topModel.sm
@@ -0,0 +1,97 @@
+// File generated by SBML-to-PRISM converter
+// Original file: SimpleHierchyModel/topModel.xml
+// @GeneticLogicLab
+
+ctmc
+
+// const int MAX_AMOUNT = ADD VALUE 
+
+// Compartment size
+const double Cell = 1.0;
+
+// Model parameters
+const double kr_f = 0.5; // Forward repression binding rate
+const double kr_r = 1.0; // Reverse repression binding rate
+const double ka_f = 0.0033; // Forward activation binding rate
+const double ka_r = 1.0; // Reverse activation binding rate
+const double ko_f = 0.033; // Forward RNAP binding rate
+const double ko_r = 1.0; // Reverse RNAP binding rate
+const double kao_f = 1.0; // Forward activated RNAP binding rate
+const double kao_r = 1.0; // Reverse activated RNAP binding rate
+const double nc = 2.0; // Stoichiometry of binding
+const double nr = 30.0; // Initial RNAP count
+const double ko = 0.05; // Open complex production rate
+const double kb = 1.0E-4; // Basal production rate
+const double ng = 2.0; // Initial promoter count
+const double np = 10.0; // Stoichiometry of production
+const double ka = 0.25; // Activated production rate
+const double kd = 0.0075; // Degradation rate
+const double C1__kr_f = 0.5; // Forward repression binding rate
+const double C1__kr_r = 1.0; // Reverse repression binding rate
+const double C1__ka_f = 0.0033; // Forward activation binding rate
+const double C1__ka_r = 1.0; // Reverse activation binding rate
+const double C1__ko_f = 0.033; // Forward RNAP binding rate
+const double C1__ko_r = 1.0; // Reverse RNAP binding rate
+const double C1__kao_f = 1.0; // Forward activated RNAP binding rate
+const double C1__kao_r = 1.0; // Reverse activated RNAP binding rate
+const double C1__nc = 2.0; // Stoichiometry of binding
+const double C1__nr = 30.0; // Initial RNAP count
+const double C1__ko = 0.05; // Open complex production rate
+const double C1__kb = 1.0E-4; // Basal production rate
+const double C1__ng = 2.0; // Initial promoter count
+const double C1__np = 10.0; // Stoichiometry of production
+const double C1__ka = 0.25; // Activated production rate
+const double C1__kd = 0.0075; // Degradation rate
+
+// Species S2
+// const int S2_MAX = MAX_AMOUNT;
+module S2
+
+  // S2 : [0..S2_MAX] init 60;
+  S2  :  int init 60;
+
+
+endmodule
+
+// Species S3
+// const int S3_MAX = MAX_AMOUNT;
+module S3
+
+  // S3 : [0..S3_MAX] init 0;
+  S3  :  int init 0;
+
+		// C1__Production_P0
+		[C1__Production_P0] S3 >= 0 -> (S3'=S3+10);
+		// Degradation_S3
+		[Degradation_S3] S3 > 0 -> (S3'=S3-1);
+
+endmodule
+
+// Species C1__P0
+// const int C1__P0_MAX = MAX_AMOUNT;
+module C1__P0
+
+  // C1__P0 : [0..C1__P0_MAX] init 2;
+  C1__P0  :  int init 2;
+
+
+endmodule
+
+// Reaction rates
+module reaction_rates
+
+		// C1__Production_P0:  ->  S3 
+		[C1__Production_P0]  ((C1__P0 * ((((C1__kb * C1__ko_f) / C1__ko_r) * C1__nr) + ((((C1__ka * C1__kao_f) / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc)))) / ((1 + ((C1__ko_f / C1__ko_r) * C1__nr)) + (((C1__kao_f / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc)))) > 0 -> (((C1__P0 * ((((C1__kb * C1__ko_f) / C1__ko_r) * C1__nr) + ((((C1__ka * C1__kao_f) / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc)))) / ((1 + ((C1__ko_f / C1__ko_r) * C1__nr)) + (((C1__kao_f / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc))))) : true;
+
+		// Degradation_S3:  ->  
+		[Degradation_S3]  (C1__kd * S3) > 0 -> ((C1__kd * S3)) : true;
+
+endmodule
+
+// Reward structures (one per species)
+// Reward 1: S2
+rewards "S2" true : S2; endrewards
+// Reward 2: S3
+rewards "S3" true : S3; endrewards
+// Reward 3: C1__P0
+rewards "C1__P0" true : C1__P0; endrewards
diff --git a/prismtest/SimpleHierchyModel/topModel.xml b/prismtest/SimpleHierchyModel/topModel.xml
new file mode 100644
index 000000000..99d9008af
--- /dev/null
+++ b/prismtest/SimpleHierchyModel/topModel.xml
@@ -0,0 +1,132 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <comp:listOfExternalModelDefinitions xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+    <comp:externalModelDefinition comp:id="DSensor" comp:md5="2b2abc20e4c21f932e52e1ff6c71104c" comp:source="DSensor.xml"/>
+  </comp:listOfExternalModelDefinitions>
+  <model id="topModel" metaid="iBioSim1">
+    <comp:listOfSubmodels xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:submodel comp:id="C1" comp:modelRef="DSensor" metaid="iBioSim17"/>
+    </comp:listOfSubmodels>
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__C1" layout:reference="C1">
+            <layout:boundingBox>
+              <layout:position layout:x="350" layout:y="160"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__S2" layout:species="S2">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="140"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S3" layout:species="S3">
+            <layout:boundingBox>
+              <layout:position layout:x="553" layout:y="143"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__C1" layout:id="TextGlyph__C1" layout:text="C1">
+            <layout:boundingBox>
+              <layout:position layout:x="350" layout:y="160"/>
+              <layout:dimensions layout:height="40" layout:width="80"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__S2" layout:id="TextGlyph__S2" layout:text="S2">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="140"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__S3" layout:id="TextGlyph__S3" layout:text="S3">
+            <layout:boundingBox>
+              <layout:position layout:x="553" layout:y="143"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions/>
+    <listOfUnitDefinitions/>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3">
+        <comp:listOfReplacedElements xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+          <comp:replacedElement comp:portRef="compartment__Cell" comp:submodelRef="C1"/>
+        </comp:listOfReplacedElements>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S2" initialAmount="60" metaid="iBioSim18">
+        <comp:listOfReplacedElements xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+          <comp:replacedElement comp:portRef="input__D" comp:submodelRef="C1"/>
+        </comp:listOfReplacedElements>
+      </species>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S3" initialAmount="0" metaid="iBioSim19">
+        <comp:replacedBy xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:portRef="output__S1" comp:submodelRef="C1"/>
+      </species>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim2" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim3" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim4" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim5" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim6" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim7" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim8" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim9" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim10" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim11" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim12" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim13" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim14" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim15" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim16" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="kd" name="Degradation rate" value="0.0075"/>
+    </listOfParameters>
+    <listOfInitialAssignments/>
+    <listOfConstraints/>
+    <listOfReactions>
+      <reaction compartment="Cell" id="Degradation_S3" reversible="false" sboTerm="SBO:0000179">
+        <comp:replacedBy xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:portRef="Degradation_S1" comp:submodelRef="C1"/>
+        <listOfReactants>
+          <speciesReference constant="true" species="S3" stoichiometry="1"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> S3 </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+    <listOfEvents/>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/SimplerChem.xml b/prismtest/SimplerChem.xml
new file mode 100644
index 000000000..574cb3a03
--- /dev/null
+++ b/prismtest/SimplerChem.xml
@@ -0,0 +1,139 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="SimplerChem" metaid="iBioSim3">
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="659" layout:y="175"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+            <layout:listOfReferenceGlyphs>
+              <layout:referenceGlyph layout:glyph="Glyph__S0" layout:id="Glyph__c0__substrate__S0" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="421" layout:y="226"/>
+                      <layout:end layout:x="684" layout:y="195"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+            </layout:listOfReferenceGlyphs>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__S0" layout:species="S0">
+            <layout:boundingBox>
+              <layout:position layout:x="371" layout:y="211"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__S0" layout:id="TextGlyph__S0" layout:text="S0">
+            <layout:boundingBox>
+              <layout:position layout:x="371" layout:y="211"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="659" layout:y="175"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions>
+      <functionDefinition id="F" name="Eventually Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">        
+          <lambda>
+            <bvar>
+              <ci> t </ci>
+            </bvar>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <or/>
+              <apply>
+                <not/>
+                <ci> t </ci>
+              </apply>
+              <apply>
+                <not/>
+                <ci> x </ci>
+              </apply>
+            </apply>
+          </lambda>
+        </math>
+            </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S0" initialAmount="50" metaid="iBioSim1"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kd" metaid="iBioSim2" name="Degradation rate" value="0.0075"/>
+    </listOfParameters>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">        
+          <apply>
+            <ci> F </ci>
+            <apply>
+              <leq/>
+              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+              <cn type="integer"> 100 </cn>
+            </apply>
+            <apply>
+              <lt/>
+              <ci> S0 </ci>
+              <cn type="integer"> 1 </cn>
+            </apply>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="Degradation_S0" metaid="iBioSim4" reversible="false" sboTerm="SBO:0000179">
+        <listOfReactants>
+          <speciesReference constant="true" species="S0" stoichiometry="1"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">          
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> S0 </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
\ No newline at end of file
diff --git a/prismtest/Speed_Independent_10_10.xml b/prismtest/Speed_Independent_10_10.xml
new file mode 100644
index 000000000..7b0a500b1
--- /dev/null
+++ b/prismtest/Speed_Independent_10_10.xml
@@ -0,0 +1,1770 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="2" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="Speed_Independent" metaid="iBioSim11">
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__A" comp:idRef="A" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="input__B" comp:idRef="B" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="output__C" comp:idRef="C" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="reaction__Degradation_C" comp:idRef="Degradation_C" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="527" layout:y="313"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+            <layout:listOfReferenceGlyphs>
+              <layout:referenceGlyph layout:glyph="Glyph__S3" layout:id="Glyph__c0__substrate__S3" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="650" layout:y="52"/>
+                      <layout:end layout:x="552" layout:y="333"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+              <layout:referenceGlyph layout:glyph="Glyph__S2" layout:id="Glyph__c0__substrate__S2" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="950" layout:y="120"/>
+                      <layout:end layout:x="552" layout:y="333"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+            </layout:listOfReferenceGlyphs>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__A" layout:species="A">
+            <layout:boundingBox>
+              <layout:position layout:x="30" layout:y="180"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S1" layout:species="S1">
+            <layout:boundingBox>
+              <layout:position layout:x="600" layout:y="105"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S2" layout:species="S2">
+            <layout:boundingBox>
+              <layout:position layout:x="900" layout:y="105"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S3" layout:species="S3">
+            <layout:boundingBox>
+              <layout:position layout:x="600" layout:y="37"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__S4" layout:species="S4">
+            <layout:boundingBox>
+              <layout:position layout:x="300" layout:y="75"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
+            <layout:boundingBox>
+              <layout:position layout:x="190" layout:y="260"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__Y" layout:species="Y">
+            <layout:boundingBox>
+              <layout:position layout:x="300" layout:y="135"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__Z" layout:species="Z">
+            <layout:boundingBox>
+              <layout:position layout:x="900" layout:y="15"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
+            <layout:boundingBox>
+              <layout:position layout:x="880" layout:y="360"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P10" layout:species="P10">
+            <layout:boundingBox>
+              <layout:position layout:x="603" layout:y="62"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P1" layout:species="P1">
+            <layout:boundingBox>
+              <layout:position layout:x="150" layout:y="45"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P2" layout:species="P2">
+            <layout:boundingBox>
+              <layout:position layout:x="150" layout:y="105"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P3" layout:species="P3">
+            <layout:boundingBox>
+              <layout:position layout:x="450" layout:y="0"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P4" layout:species="P4">
+            <layout:boundingBox>
+              <layout:position layout:x="450" layout:y="60"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P5" layout:species="P5">
+            <layout:boundingBox>
+              <layout:position layout:x="750" layout:y="120"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P6" layout:species="P6">
+            <layout:boundingBox>
+              <layout:position layout:x="940" layout:y="190"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P7" layout:species="P7">
+            <layout:boundingBox>
+              <layout:position layout:x="450" layout:y="150"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P8" layout:species="P8">
+            <layout:boundingBox>
+              <layout:position layout:x="750" layout:y="60"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P9" layout:species="P9">
+            <layout:boundingBox>
+              <layout:position layout:x="900" layout:y="70"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__X" layout:species="X">
+            <layout:boundingBox>
+              <layout:position layout:x="300" layout:y="15"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_S4" layout:reaction="Degradation_S4">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="30"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_S4__substrate__S4" layout:role="substrate" layout:speciesGlyph="Glyph__S4">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="350" layout:y="90"/>
+                      <layout:end layout:x="30" layout:y="40"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_S1" layout:reaction="Degradation_S1">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="60"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_S1__substrate__S1" layout:role="substrate" layout:speciesGlyph="Glyph__S1">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="650" layout:y="120"/>
+                      <layout:end layout:x="50" layout:y="70"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_Z" layout:reaction="Degradation_Z">
+            <layout:boundingBox>
+              <layout:position layout:x="60" layout:y="90"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_Z__substrate__Z" layout:role="substrate" layout:speciesGlyph="Glyph__Z">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="950" layout:y="30"/>
+                      <layout:end layout:x="70" layout:y="100"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_C" layout:reaction="Degradation_C">
+            <layout:boundingBox>
+              <layout:position layout:x="80" layout:y="120"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_C__substrate__C" layout:role="substrate" layout:speciesGlyph="Glyph__C">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="930" layout:y="375"/>
+                      <layout:end layout:x="90" layout:y="130"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_X" layout:reaction="Degradation_X">
+            <layout:boundingBox>
+              <layout:position layout:x="100" layout:y="150"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_X__substrate__X" layout:role="substrate" layout:speciesGlyph="Glyph__X">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="350" layout:y="30"/>
+                      <layout:end layout:x="110" layout:y="160"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_S2" layout:reaction="Degradation_S2">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="180"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_S2__substrate__S2" layout:role="substrate" layout:speciesGlyph="Glyph__S2">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="950" layout:y="120"/>
+                      <layout:end layout:x="130" layout:y="190"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_S3" layout:reaction="Degradation_S3">
+            <layout:boundingBox>
+              <layout:position layout:x="140" layout:y="210"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_S3__substrate__S3" layout:role="substrate" layout:speciesGlyph="Glyph__S3">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="650" layout:y="52"/>
+                      <layout:end layout:x="150" layout:y="220"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_Y" layout:reaction="Degradation_Y">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="240"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_Y__substrate__Y" layout:role="substrate" layout:speciesGlyph="Glyph__Y">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="350" layout:y="150"/>
+                      <layout:end layout:x="170" layout:y="250"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P10__Production__S4">
+            <layout:boundingBox>
+              <layout:position layout:x="350" layout:y="90"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P10__Production__S4" layout:role="product" layout:speciesGlyph="Glyph__S4">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="653" layout:y="77"/>
+                      <layout:end layout:x="350" layout:y="90"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__S2__repression__P10">
+            <layout:boundingBox>
+              <layout:position layout:x="653" layout:y="77"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__S2__repression__P10" layout:role="product" layout:speciesGlyph="Glyph__P10">
+                <layout:curve>
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+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P2" layout:id="TextGlyph__P2" layout:text="P2">
+            <layout:boundingBox>
+              <layout:position layout:x="150" layout:y="105"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P3" layout:id="TextGlyph__P3" layout:text="P3">
+            <layout:boundingBox>
+              <layout:position layout:x="450" layout:y="0"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P4" layout:id="TextGlyph__P4" layout:text="P4">
+            <layout:boundingBox>
+              <layout:position layout:x="450" layout:y="60"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P5" layout:id="TextGlyph__P5" layout:text="P5">
+            <layout:boundingBox>
+              <layout:position layout:x="750" layout:y="120"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P6" layout:id="TextGlyph__P6" layout:text="P6">
+            <layout:boundingBox>
+              <layout:position layout:x="940" layout:y="190"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P7" layout:id="TextGlyph__P7" layout:text="P7">
+            <layout:boundingBox>
+              <layout:position layout:x="450" layout:y="150"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P8" layout:id="TextGlyph__P8" layout:text="P8">
+            <layout:boundingBox>
+              <layout:position layout:x="750" layout:y="60"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P9" layout:id="TextGlyph__P9" layout:text="P9">
+            <layout:boundingBox>
+              <layout:position layout:x="900" layout:y="70"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__X" layout:id="TextGlyph__X" layout:text="X">
+            <layout:boundingBox>
+              <layout:position layout:x="300" layout:y="15"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="527" layout:y="313"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_S4" layout:id="TextGlyph__Degradation_S4" layout:text="Degradation_S4">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="30"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_S1" layout:id="TextGlyph__Degradation_S1" layout:text="Degradation_S1">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="60"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_Z" layout:id="TextGlyph__Degradation_Z" layout:text="Degradation_Z">
+            <layout:boundingBox>
+              <layout:position layout:x="60" layout:y="90"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_C" layout:id="TextGlyph__Degradation_C" layout:text="Degradation_C">
+            <layout:boundingBox>
+              <layout:position layout:x="80" layout:y="120"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_X" layout:id="TextGlyph__Degradation_X" layout:text="Degradation_X">
+            <layout:boundingBox>
+              <layout:position layout:x="100" layout:y="150"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_S2" layout:id="TextGlyph__Degradation_S2" layout:text="Degradation_S2">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="180"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_S3" layout:id="TextGlyph__Degradation_S3" layout:text="Degradation_S3">
+            <layout:boundingBox>
+              <layout:position layout:x="140" layout:y="210"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_Y" layout:id="TextGlyph__Degradation_Y" layout:text="Degradation_Y">
+            <layout:boundingBox>
+              <layout:position layout:x="160" layout:y="240"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions>
+      <functionDefinition id="F" name="Eventually Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> t </ci>
+            </bvar>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <or/>
+              <apply>
+                <not/>
+                <ci> t </ci>
+              </apply>
+              <apply>
+                <not/>
+                <ci> x </ci>
+              </apply>
+            </apply>
+          </lambda>
+        </math>
+            </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="A" initialAmount="0" metaid="iBioSim1"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S1" initialAmount="70" metaid="iBioSim3"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S2" initialAmount="0" metaid="iBioSim4"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S3" initialAmount="70" metaid="iBioSim5"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S4" initialAmount="130" metaid="iBioSim6"/>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="B" initialAmount="120" metaid="iBioSim7"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Y" initialAmount="0" metaid="iBioSim8"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Z" initialAmount="0" metaid="iBioSim9"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="C" initialAmount="70" metaid="iBioSim10"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P10" initialAmount="2" metaid="iBioSim12" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P1" initialAmount="2" metaid="iBioSim14" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P2" initialAmount="2" metaid="iBioSim16" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P3" initialAmount="2" metaid="iBioSim18" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P4" initialAmount="2" metaid="iBioSim20" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P5" initialAmount="2" metaid="iBioSim22" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P6" initialAmount="2" metaid="iBioSim24" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P7" initialAmount="2" metaid="iBioSim26" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P8" initialAmount="2" metaid="iBioSim28" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P9" initialAmount="2" metaid="iBioSim30" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="X" initialAmount="70" metaid="iBioSim33"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kd" metaid="iBioSim2" name="Degradation rate" value="0.00075"/>
+      <parameter constant="true" id="kr_f" metaid="iBioSim13" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim34" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim35" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim36" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim37" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim38" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim39" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim40" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim41" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim42" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim43" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim44" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim45" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim46" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim47" name="Activated production rate" value="0.25"/>
+    </listOfParameters>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <ci> F </ci>
+            <apply>
+              <leq/>
+              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+              <cn type="integer"> 2100 </cn>
+            </apply>
+            <apply>
+              <and/>
+              <apply>
+                <gt/>
+                <ci> S2 </ci>
+                <cn type="integer"> 80 </cn>
+              </apply>
+              <apply>
+                <lt/>
+                <ci> S3 </ci>
+                <cn type="integer"> 20 </cn>
+              </apply>
+            </apply>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="Degradation_S4" metaid="iBioSim48" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="S4" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> S4 </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_S1" metaid="iBioSim49" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="S1" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> S1 </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_Z" metaid="iBioSim53" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> Z </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_C" metaid="iBioSim54" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="C" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> C </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P10" metaid="iBioSim32" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S4" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P10"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="S2"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P10 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> S2 </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P1" metaid="iBioSim15" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S4" stoichiometry="10"/>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P1 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> A </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P2" metaid="iBioSim17" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S4" stoichiometry="10"/>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P2 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> B </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P3" metaid="iBioSim19" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S3" stoichiometry="10"/>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="S4"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P3 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> S4 </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P4" metaid="iBioSim21" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S1" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P4 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> X </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P5" metaid="iBioSim23" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S2" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="S1"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P5 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> S1 </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P6" metaid="iBioSim25" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S3" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="S2"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P6 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> S2 </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P7" metaid="iBioSim27" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S1" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P7 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> Y </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P8" metaid="iBioSim29" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="S2" stoichiometry="10"/>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="S3"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P8 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> S3 </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P9" metaid="iBioSim31" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="C" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P9"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <times/>
+                  <apply>
+                    <times/>
+                    <ci> P9 </ci>
+                    <ci> ko </ci>
+                  </apply>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> Z </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_X" metaid="iBioSim55" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> X </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_S2" metaid="iBioSim50" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="S2" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> S2 </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_S3" metaid="iBioSim51" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="S3" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> S3 </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_Y" metaid="iBioSim52" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> Y </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/prismtest/Toggle_10_10.props b/prismtest/Toggle_10_10.props
new file mode 100644
index 000000000..4dd9df6ec
--- /dev/null
+++ b/prismtest/Toggle_10_10.props
@@ -0,0 +1,5 @@
+// File generated by SBML-to-PRISM converter
+// Original file: Toggle_10_10.xml
+// @GeneticLogicLab
+
+P=? [F<=2100 ((Z > 80) & (Y < 40))]
\ No newline at end of file
diff --git a/prismtest/Toggle_10_10.sm b/prismtest/Toggle_10_10.sm
new file mode 100644
index 000000000..e86b8e68c
--- /dev/null
+++ b/prismtest/Toggle_10_10.sm
@@ -0,0 +1,320 @@
+// File generated by SBML-to-PRISM converter
+// Original file: Toggle_10_10.xml
+// @GeneticLogicLab
+
+ctmc
+
+// const int MAX_AMOUNT = ADD VALUE 
+
+// Compartment size
+const double Cell = 1.0;
+
+// Model parameters
+const double kr_f = 0.5; // Forward repression binding rate
+const double kr_r = 1.0; // Reverse repression binding rate
+const double ka_f = 0.0033; // Forward activation binding rate
+const double ka_r = 1.0; // Reverse activation binding rate
+const double ko_f = 0.033; // Forward RNAP binding rate
+const double ko_r = 1.0; // Reverse RNAP binding rate
+const double kao_f = 1.0; // Forward activated RNAP binding rate
+const double kao_r = 1.0; // Reverse activated RNAP binding rate
+const double nc = 2.0; // Stoichiometry of binding
+const double nr = 30.0; // Initial RNAP count
+const double ko = 0.05; // Open complex production rate
+const double kb = 1.0E-4; // Basal production rate
+const double ng = 2.0; // Initial promoter count
+const double np = 10.0; // Stoichiometry of production
+const double ka = 0.25; // Activated production rate
+const double kd = 7.5E-4; // Degradation rate
+
+// Species _A
+// const int _A_MAX = MAX_AMOUNT;
+module _A
+
+  // _A : [0.._A_MAX] init 0;
+  _A  :  int init 0;
+
+
+endmodule
+
+// Species D
+// const int D_MAX = MAX_AMOUNT;
+module D
+
+  // D : [0..D_MAX] init 70;
+  D  :  int init 70;
+
+		// Production_P1
+		[Production_P1] D >= 0 -> (D'=D+10);
+		// Degradation_D
+		[Degradation_D] D > 9 -> (D'=D-10);
+
+endmodule
+
+// Species B
+// const int B_MAX = MAX_AMOUNT;
+module B
+
+  // B : [0..B_MAX] init 120;
+  B  :  int init 120;
+
+
+endmodule
+
+// Species Y
+// const int Y_MAX = MAX_AMOUNT;
+module Y
+
+  // Y : [0..Y_MAX] init 70;
+  Y  :  int init 70;
+
+		// Production_P3
+		[Production_P3] Y >= 0 -> (Y'=Y+10);
+		// Production_P5
+		[Production_P5] Y >= 0 -> (Y'=Y+10);
+		// Degradation_Y
+		[Degradation_Y] Y > 9 -> (Y'=Y-10);
+
+endmodule
+
+// Species _E
+// const int _E_MAX = MAX_AMOUNT;
+module _E
+
+  // _E : [0.._E_MAX] init 0;
+  _E  :  int init 0;
+
+		// Production_P2
+		[Production_P2] _E >= 0 -> (_E'=_E+10);
+		// Degradation_E
+		[Degradation_E] _E > 9 -> (_E'=_E-10);
+
+endmodule
+
+// Species _X
+// const int _X_MAX = MAX_AMOUNT;
+module _X
+
+  // _X : [0.._X_MAX] init 70;
+  _X  :  int init 70;
+
+		// Production_P1
+		[Production_P1] _X >= 0 -> (_X'=_X+10);
+		// Production_P2
+		[Production_P2] _X >= 0 -> (_X'=_X+10);
+		// Degradation_X
+		[Degradation_X] _X > 9 -> (_X'=_X-10);
+
+endmodule
+
+// Species FF
+// const int FF_MAX = MAX_AMOUNT;
+module FF
+
+  // FF : [0..FF_MAX] init 70;
+  FF  :  int init 70;
+
+		// Production_P8
+		[Production_P8] FF >= 0 -> (FF'=FF+10);
+		// Production_P7
+		[Production_P7] FF >= 0 -> (FF'=FF+10);
+		// Degradation_FF
+		[Degradation_FF] FF > 9 -> (FF'=FF-10);
+
+endmodule
+
+// Species Z
+// const int Z_MAX = MAX_AMOUNT;
+module Z
+
+  // Z : [0..Z_MAX] init 0;
+  Z  :  int init 0;
+
+		// Production_P4
+		[Production_P4] Z >= 0 -> (Z'=Z+10);
+		// Production_P6
+		[Production_P6] Z >= 0 -> (Z'=Z+10);
+		// Degradation_Z
+		[Degradation_Z] Z > 9 -> (Z'=Z-10);
+
+endmodule
+
+// Species _C
+// const int _C_MAX = MAX_AMOUNT;
+module _C
+
+  // _C : [0.._C_MAX] init 70;
+  _C  :  int init 70;
+
+		// Production_P5
+		[Production_P5] _C >= 0 -> (_C'=_C+10);
+		// Degradation_C
+		[Degradation_C] _C > 9 -> (_C'=_C-10);
+
+endmodule
+
+// Species P8
+// const int P8_MAX = MAX_AMOUNT;
+module P8
+
+  // P8 : [0..P8_MAX] init 2;
+  P8  :  int init 2;
+
+
+endmodule
+
+// Species P1
+// const int P1_MAX = MAX_AMOUNT;
+module P1
+
+  // P1 : [0..P1_MAX] init 2;
+  P1  :  int init 2;
+
+
+endmodule
+
+// Species P2
+// const int P2_MAX = MAX_AMOUNT;
+module P2
+
+  // P2 : [0..P2_MAX] init 2;
+  P2  :  int init 2;
+
+
+endmodule
+
+// Species P3
+// const int P3_MAX = MAX_AMOUNT;
+module P3
+
+  // P3 : [0..P3_MAX] init 2;
+  P3  :  int init 2;
+
+
+endmodule
+
+// Species P4
+// const int P4_MAX = MAX_AMOUNT;
+module P4
+
+  // P4 : [0..P4_MAX] init 2;
+  P4  :  int init 2;
+
+
+endmodule
+
+// Species P5
+// const int P5_MAX = MAX_AMOUNT;
+module P5
+
+  // P5 : [0..P5_MAX] init 2;
+  P5  :  int init 2;
+
+
+endmodule
+
+// Species P6
+// const int P6_MAX = MAX_AMOUNT;
+module P6
+
+  // P6 : [0..P6_MAX] init 2;
+  P6  :  int init 2;
+
+
+endmodule
+
+// Species P7
+// const int P7_MAX = MAX_AMOUNT;
+module P7
+
+  // P7 : [0..P7_MAX] init 2;
+  P7  :  int init 2;
+
+
+endmodule
+
+// Reaction rates
+module reaction_rates
+
+		// Production_P8:  ->  FF 
+		[Production_P8]  (((((P8 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) *_E) , nc))) > 0 -> ((((((P8 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) *_E) , nc)))) : true;
+
+		// Production_P1:  ->  D _X 
+		[Production_P1]  (((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) *_A) , nc))) > 0 -> ((((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) *_A) , nc)))) : true;
+
+		// Production_P2:  ->  _E _X 
+		[Production_P2]  (((((P2 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * B) , nc))) > 0 -> ((((((P2 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * B) , nc)))) : true;
+
+		// Production_P3:  ->  Y 
+		[Production_P3]  (((((P3 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) *_X) , nc))) > 0 -> ((((((P3 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) *_X) , nc)))) : true;
+
+		// Production_P4:  ->  Z 
+		[Production_P4]  (((((P4 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * FF) , nc))) > 0 -> ((((((P4 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * FF) , nc)))) : true;
+
+		// Production_P5:  ->  _C Y 
+		[Production_P5]  (((((P5 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * Z) , nc))) > 0 -> ((((((P5 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * Z) , nc)))) : true;
+
+		// Production_P6:  ->  Z 
+		[Production_P6]  (((((P6 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * Y) , nc))) > 0 -> ((((((P6 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * Y) , nc)))) : true;
+
+		// Production_P7:  ->  FF 
+		[Production_P7]  (((((P7 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * D) , nc))) > 0 -> ((((((P7 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * D) , nc)))) : true;
+
+		// Degradation_E:  ->  
+		[Degradation_E]  (kd *_E) > 0 -> ((kd *_E)) : true;
+
+		// Degradation_C:  ->  
+		[Degradation_C]  (kd *_C) > 0 -> ((kd *_C)) : true;
+
+		// Degradation_X:  ->  
+		[Degradation_X]  (kd *_X) > 0 -> ((kd *_X)) : true;
+
+		// Degradation_D:  ->  
+		[Degradation_D]  (kd * D) > 0 -> ((kd * D)) : true;
+
+		// Degradation_FF:  ->  
+		[Degradation_FF]  (kd * FF) > 0 -> ((kd * FF)) : true;
+
+		// Degradation_Y:  ->  
+		[Degradation_Y]  (kd * Y) > 0 -> ((kd * Y)) : true;
+
+		// Degradation_Z:  ->  
+		[Degradation_Z]  (kd * Z) > 0 -> ((kd * Z)) : true;
+
+endmodule
+
+// Reward structures (one per species)
+// Reward 1: _A
+rewards "_A" true : _A; endrewards
+// Reward 2: D
+rewards "D" true : D; endrewards
+// Reward 3: B
+rewards "B" true : B; endrewards
+// Reward 4: Y
+rewards "Y" true : Y; endrewards
+// Reward 5: _E
+rewards "_E" true : _E; endrewards
+// Reward 6: _X
+rewards "_X" true : _X; endrewards
+// Reward 7: FF
+rewards "FF" true : FF; endrewards
+// Reward 8: Z
+rewards "Z" true : Z; endrewards
+// Reward 9: _C
+rewards "_C" true : _C; endrewards
+// Reward 10: P8
+rewards "P8" true : P8; endrewards
+// Reward 11: P1
+rewards "P1" true : P1; endrewards
+// Reward 12: P2
+rewards "P2" true : P2; endrewards
+// Reward 13: P3
+rewards "P3" true : P3; endrewards
+// Reward 14: P4
+rewards "P4" true : P4; endrewards
+// Reward 15: P5
+rewards "P5" true : P5; endrewards
+// Reward 16: P6
+rewards "P6" true : P6; endrewards
+// Reward 17: P7
+rewards "P7" true : P7; endrewards
diff --git a/prismtest/Toggle_10_10.xml b/prismtest/Toggle_10_10.xml
new file mode 100644
index 000000000..59265dc8b
--- /dev/null
+++ b/prismtest/Toggle_10_10.xml
@@ -0,0 +1,1478 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="2" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+  <model id="Toggle_Switch_C" metaid="iBioSim42">
+    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="input__A" comp:idRef="A" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="input__B" comp:idRef="B" sboTerm="SBO:0000600"/>
+      <comp:port comp:id="reaction__Degradation_C" comp:idRef="Degradation_C" sboTerm="SBO:0000601"/>
+      <comp:port comp:id="output__C" comp:idRef="C" sboTerm="SBO:0000601"/>
+    </comp:listOfPorts>
+    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+      <layout:layout layout:id="iBioSim">
+        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
+        <layout:listOfAdditionalGraphicalObjects>
+          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="831" layout:y="93"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+            <layout:listOfReferenceGlyphs>
+              <layout:referenceGlyph layout:glyph="Glyph__Y" layout:id="Glyph__c0__substrate__Y" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="660" layout:y="315"/>
+                      <layout:end layout:x="856" layout:y="113"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+              <layout:referenceGlyph layout:glyph="Glyph__Z" layout:id="Glyph__c0__substrate__Z" layout:role="substrate">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="940" layout:y="265"/>
+                      <layout:end layout:x="856" layout:y="113"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:referenceGlyph>
+            </layout:listOfReferenceGlyphs>
+          </layout:generalGlyph>
+        </layout:listOfAdditionalGraphicalObjects>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="Glyph__A" layout:species="A">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="50"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__D" layout:species="D">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="200"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
+            <layout:boundingBox>
+              <layout:position layout:x="200" layout:y="50"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__Y" layout:species="Y">
+            <layout:boundingBox>
+              <layout:position layout:x="610" layout:y="300"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__E" layout:species="E">
+            <layout:boundingBox>
+              <layout:position layout:x="420" layout:y="30"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__X" layout:species="X">
+            <layout:boundingBox>
+              <layout:position layout:x="260" layout:y="210"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__FF" layout:species="FF">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="380"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__Z" layout:species="Z">
+            <layout:boundingBox>
+              <layout:position layout:x="890" layout:y="250"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
+            <layout:boundingBox>
+              <layout:position layout:x="540" layout:y="80"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P8" layout:species="P8">
+            <layout:boundingBox>
+              <layout:position layout:x="430" layout:y="380"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P1" layout:species="P1">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="120"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P2" layout:species="P2">
+            <layout:boundingBox>
+              <layout:position layout:x="200" layout:y="120"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P3" layout:species="P3">
+            <layout:boundingBox>
+              <layout:position layout:x="270" layout:y="280"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P4" layout:species="P4">
+            <layout:boundingBox>
+              <layout:position layout:x="560" layout:y="190"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P5" layout:species="P5">
+            <layout:boundingBox>
+              <layout:position layout:x="550" layout:y="140"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P6" layout:species="P6">
+            <layout:boundingBox>
+              <layout:position layout:x="610" layout:y="380"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="Glyph__P7" layout:species="P7">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="280"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_E" layout:reaction="Degradation_E">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="30"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_E__substrate__E" layout:role="substrate" layout:speciesGlyph="Glyph__E">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="470" layout:y="45"/>
+                      <layout:end layout:x="30" layout:y="40"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_C" layout:reaction="Degradation_C">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="60"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_C__substrate__C" layout:role="substrate" layout:speciesGlyph="Glyph__C">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="590" layout:y="95"/>
+                      <layout:end layout:x="50" layout:y="70"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_X" layout:reaction="Degradation_X">
+            <layout:boundingBox>
+              <layout:position layout:x="60" layout:y="90"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_X__substrate__X" layout:role="substrate" layout:speciesGlyph="Glyph__X">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="310" layout:y="225"/>
+                      <layout:end layout:x="70" layout:y="100"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_D" layout:reaction="Degradation_D">
+            <layout:boundingBox>
+              <layout:position layout:x="80" layout:y="120"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_D__substrate__D" layout:role="substrate" layout:speciesGlyph="Glyph__D">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="215"/>
+                      <layout:end layout:x="90" layout:y="130"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_FF" layout:reaction="Degradation_FF">
+            <layout:boundingBox>
+              <layout:position layout:x="100" layout:y="150"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_FF__substrate__FF" layout:role="substrate" layout:speciesGlyph="Glyph__FF">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="395"/>
+                      <layout:end layout:x="110" layout:y="160"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_Y" layout:reaction="Degradation_Y">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="180"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_Y__substrate__Y" layout:role="substrate" layout:speciesGlyph="Glyph__Y">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="660" layout:y="315"/>
+                      <layout:end layout:x="130" layout:y="190"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Degradation_Z" layout:reaction="Degradation_Z">
+            <layout:boundingBox>
+              <layout:position layout:x="140" layout:y="210"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_Z__substrate__Z" layout:role="substrate" layout:speciesGlyph="Glyph__Z">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="940" layout:y="265"/>
+                      <layout:end layout:x="150" layout:y="220"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P8__Production__FF">
+            <layout:boundingBox>
+              <layout:position layout:x="180" layout:y="395"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P8__Production__FF" layout:role="product" layout:speciesGlyph="Glyph__FF">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="480" layout:y="395"/>
+                      <layout:end layout:x="180" layout:y="395"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__E__repression__P8">
+            <layout:boundingBox>
+              <layout:position layout:x="480" layout:y="395"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__E__repression__P8" layout:role="product" layout:speciesGlyph="Glyph__P8">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="470" layout:y="45"/>
+                      <layout:end layout:x="480" layout:y="395"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P1__Production__D">
+            <layout:boundingBox>
+              <layout:position layout:x="50" layout:y="215"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P1__Production__D" layout:role="product" layout:speciesGlyph="Glyph__D">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="90" layout:y="135"/>
+                      <layout:end layout:x="50" layout:y="215"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P1__Production__X">
+            <layout:boundingBox>
+              <layout:position layout:x="310" layout:y="225"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P1__Production__X" layout:role="product" layout:speciesGlyph="Glyph__X">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="90" layout:y="135"/>
+                      <layout:end layout:x="310" layout:y="225"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__A__repression__P1">
+            <layout:boundingBox>
+              <layout:position layout:x="90" layout:y="135"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__A__repression__P1" layout:role="product" layout:speciesGlyph="Glyph__P1">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="90" layout:y="65"/>
+                      <layout:end layout:x="90" layout:y="135"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P2__Production__E">
+            <layout:boundingBox>
+              <layout:position layout:x="470" layout:y="45"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P2__Production__E" layout:role="product" layout:speciesGlyph="Glyph__E">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="250" layout:y="135"/>
+                      <layout:end layout:x="470" layout:y="45"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P2__Production__X">
+            <layout:boundingBox>
+              <layout:position layout:x="310" layout:y="225"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P2__Production__X" layout:role="product" layout:speciesGlyph="Glyph__X">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="250" layout:y="135"/>
+                      <layout:end layout:x="310" layout:y="225"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__B__repression__P2">
+            <layout:boundingBox>
+              <layout:position layout:x="250" layout:y="135"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__B__repression__P2" layout:role="product" layout:speciesGlyph="Glyph__P2">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="250" layout:y="65"/>
+                      <layout:end layout:x="250" layout:y="135"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P3__Production__Y">
+            <layout:boundingBox>
+              <layout:position layout:x="660" layout:y="315"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P3__Production__Y" layout:role="product" layout:speciesGlyph="Glyph__Y">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="320" layout:y="295"/>
+                      <layout:end layout:x="660" layout:y="315"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__X__repression__P3">
+            <layout:boundingBox>
+              <layout:position layout:x="320" layout:y="295"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__X__repression__P3" layout:role="product" layout:speciesGlyph="Glyph__P3">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="310" layout:y="225"/>
+                      <layout:end layout:x="320" layout:y="295"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P4__Production__Z">
+            <layout:boundingBox>
+              <layout:position layout:x="940" layout:y="265"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P4__Production__Z" layout:role="product" layout:speciesGlyph="Glyph__Z">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="610" layout:y="205"/>
+                      <layout:end layout:x="940" layout:y="265"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__FF__repression__P4">
+            <layout:boundingBox>
+              <layout:position layout:x="610" layout:y="205"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__FF__repression__P4" layout:role="product" layout:speciesGlyph="Glyph__P4">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="180" layout:y="395"/>
+                      <layout:end layout:x="610" layout:y="205"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P5__Production__C">
+            <layout:boundingBox>
+              <layout:position layout:x="590" layout:y="95"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P5__Production__C" layout:role="product" layout:speciesGlyph="Glyph__C">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="600" layout:y="155"/>
+                      <layout:end layout:x="590" layout:y="95"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P5__Production__Y">
+            <layout:boundingBox>
+              <layout:position layout:x="660" layout:y="315"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P5__Production__Y" layout:role="product" layout:speciesGlyph="Glyph__Y">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="600" layout:y="155"/>
+                      <layout:end layout:x="660" layout:y="315"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Z__repression__P5">
+            <layout:boundingBox>
+              <layout:position layout:x="600" layout:y="155"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Z__repression__P5" layout:role="product" layout:speciesGlyph="Glyph__P5">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="940" layout:y="265"/>
+                      <layout:end layout:x="600" layout:y="155"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P6__Production__Z">
+            <layout:boundingBox>
+              <layout:position layout:x="940" layout:y="265"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P6__Production__Z" layout:role="product" layout:speciesGlyph="Glyph__Z">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="660" layout:y="395"/>
+                      <layout:end layout:x="940" layout:y="265"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__Y__repression__P6">
+            <layout:boundingBox>
+              <layout:position layout:x="660" layout:y="395"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Y__repression__P6" layout:role="product" layout:speciesGlyph="Glyph__P6">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="660" layout:y="315"/>
+                      <layout:end layout:x="660" layout:y="395"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__P7__Production__FF">
+            <layout:boundingBox>
+              <layout:position layout:x="180" layout:y="395"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P7__Production__FF" layout:role="product" layout:speciesGlyph="Glyph__FF">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="295"/>
+                      <layout:end layout:x="180" layout:y="395"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+          <layout:reactionGlyph layout:id="Glyph__D__repression__P7">
+            <layout:boundingBox>
+              <layout:position layout:x="50" layout:y="295"/>
+              <layout:dimensions layout:height="0" layout:width="0"/>
+            </layout:boundingBox>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__D__repression__P7" layout:role="product" layout:speciesGlyph="Glyph__P7">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xsi:type="LineSegment">
+                      <layout:start layout:x="50" layout:y="215"/>
+                      <layout:end layout:x="50" layout:y="295"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:height="425" layout:width="1070"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__A" layout:id="TextGlyph__A" layout:text="A">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="50"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__D" layout:id="TextGlyph__D" layout:text="D">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="200"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__B" layout:id="TextGlyph__B" layout:text="B">
+            <layout:boundingBox>
+              <layout:position layout:x="200" layout:y="50"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Y" layout:id="TextGlyph__Y" layout:text="Y">
+            <layout:boundingBox>
+              <layout:position layout:x="610" layout:y="300"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__E" layout:id="TextGlyph__E" layout:text="E">
+            <layout:boundingBox>
+              <layout:position layout:x="420" layout:y="30"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__X" layout:id="TextGlyph__X" layout:text="X">
+            <layout:boundingBox>
+              <layout:position layout:x="260" layout:y="210"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__FF" layout:id="TextGlyph__FF" layout:text="FF">
+            <layout:boundingBox>
+              <layout:position layout:x="130" layout:y="380"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Z" layout:id="TextGlyph__Z" layout:text="Z">
+            <layout:boundingBox>
+              <layout:position layout:x="890" layout:y="250"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__C" layout:id="TextGlyph__C" layout:text="C">
+            <layout:boundingBox>
+              <layout:position layout:x="540" layout:y="80"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P8" layout:id="TextGlyph__P8" layout:text="P8">
+            <layout:boundingBox>
+              <layout:position layout:x="430" layout:y="380"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P1" layout:id="TextGlyph__P1" layout:text="P1">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="120"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P2" layout:id="TextGlyph__P2" layout:text="P2">
+            <layout:boundingBox>
+              <layout:position layout:x="200" layout:y="120"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P3" layout:id="TextGlyph__P3" layout:text="P3">
+            <layout:boundingBox>
+              <layout:position layout:x="270" layout:y="280"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P4" layout:id="TextGlyph__P4" layout:text="P4">
+            <layout:boundingBox>
+              <layout:position layout:x="560" layout:y="190"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P5" layout:id="TextGlyph__P5" layout:text="P5">
+            <layout:boundingBox>
+              <layout:position layout:x="550" layout:y="140"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P6" layout:id="TextGlyph__P6" layout:text="P6">
+            <layout:boundingBox>
+              <layout:position layout:x="610" layout:y="380"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__P7" layout:id="TextGlyph__P7" layout:text="P7">
+            <layout:boundingBox>
+              <layout:position layout:x="0" layout:y="280"/>
+              <layout:dimensions layout:height="30" layout:width="100"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
+            <layout:boundingBox>
+              <layout:position layout:x="831" layout:y="93"/>
+              <layout:dimensions layout:height="40" layout:width="50"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_E" layout:id="TextGlyph__Degradation_E" layout:text="Degradation_E">
+            <layout:boundingBox>
+              <layout:position layout:x="20" layout:y="30"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_C" layout:id="TextGlyph__Degradation_C" layout:text="Degradation_C">
+            <layout:boundingBox>
+              <layout:position layout:x="40" layout:y="60"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_X" layout:id="TextGlyph__Degradation_X" layout:text="Degradation_X">
+            <layout:boundingBox>
+              <layout:position layout:x="60" layout:y="90"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_D" layout:id="TextGlyph__Degradation_D" layout:text="Degradation_D">
+            <layout:boundingBox>
+              <layout:position layout:x="80" layout:y="120"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_FF" layout:id="TextGlyph__Degradation_FF" layout:text="Degradation_FF">
+            <layout:boundingBox>
+              <layout:position layout:x="100" layout:y="150"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_Y" layout:id="TextGlyph__Degradation_Y" layout:text="Degradation_Y">
+            <layout:boundingBox>
+              <layout:position layout:x="120" layout:y="180"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+          <layout:textGlyph layout:graphicalObject="Glyph__Degradation_Z" layout:id="TextGlyph__Degradation_Z" layout:text="Degradation_Z">
+            <layout:boundingBox>
+              <layout:position layout:x="140" layout:y="210"/>
+              <layout:dimensions layout:height="20" layout:width="20"/>
+            </layout:boundingBox>
+          </layout:textGlyph>
+        </layout:listOfTextGlyphs>
+      </layout:layout>
+    </layout:listOfLayouts>
+    <listOfFunctionDefinitions>
+      <functionDefinition id="F" name="Eventually Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> t </ci>
+            </bvar>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <or/>
+              <apply>
+                <not/>
+                <ci> t </ci>
+              </apply>
+              <apply>
+                <not/>
+                <ci> x </ci>
+              </apply>
+            </apply>
+          </lambda>
+        </math>
+            </functionDefinition>
+    </listOfFunctionDefinitions>
+    <listOfCompartments>
+      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="A" initialAmount="0" metaid="iBioSim1"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="D" initialAmount="70" metaid="iBioSim3"/>
+      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="B" initialAmount="120" metaid="iBioSim4"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Y" initialAmount="70" metaid="iBioSim5"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="E" initialAmount="0" metaid="iBioSim6"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="X" initialAmount="70" metaid="iBioSim7"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="FF" initialAmount="70" metaid="iBioSim8"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Z" initialAmount="0" metaid="iBioSim9"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="C" initialAmount="70" metaid="iBioSim10"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P8" initialAmount="2" metaid="iBioSim11" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P1" initialAmount="2" metaid="iBioSim13" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P2" initialAmount="2" metaid="iBioSim15" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P3" initialAmount="2" metaid="iBioSim17" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P4" initialAmount="2" metaid="iBioSim19" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P5" initialAmount="2" metaid="iBioSim21" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P6" initialAmount="2" metaid="iBioSim23" sboTerm="SBO:0000590"/>
+      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P7" initialAmount="2" metaid="iBioSim25" sboTerm="SBO:0000590"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter constant="true" id="kr_f" metaid="iBioSim2" name="Forward repression binding rate" value="0.5"/>
+      <parameter constant="true" id="kr_r" metaid="iBioSim28" name="Reverse repression binding rate" value="1"/>
+      <parameter constant="true" id="ka_f" metaid="iBioSim29" name="Forward activation binding rate" value="0.0033"/>
+      <parameter constant="true" id="ka_r" metaid="iBioSim30" name="Reverse activation binding rate" value="1"/>
+      <parameter constant="true" id="ko_f" metaid="iBioSim31" name="Forward RNAP binding rate" value="0.033"/>
+      <parameter constant="true" id="ko_r" metaid="iBioSim32" name="Reverse RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_f" metaid="iBioSim33" name="Forward activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="kao_r" metaid="iBioSim34" name="Reverse activated RNAP binding rate" value="1"/>
+      <parameter constant="true" id="nc" metaid="iBioSim35" name="Stoichiometry of binding" value="2"/>
+      <parameter constant="true" id="nr" metaid="iBioSim36" name="Initial RNAP count" value="30"/>
+      <parameter constant="true" id="ko" metaid="iBioSim37" name="Open complex production rate" value="0.05"/>
+      <parameter constant="true" id="kb" metaid="iBioSim38" name="Basal production rate" value="0.0001"/>
+      <parameter constant="true" id="ng" metaid="iBioSim39" name="Initial promoter count" value="2"/>
+      <parameter constant="true" id="np" metaid="iBioSim40" name="Stoichiometry of production" value="10"/>
+      <parameter constant="true" id="ka" metaid="iBioSim41" name="Activated production rate" value="0.25"/>
+      <parameter constant="true" id="kd" metaid="iBioSim12" name="Degradation rate" value="0.00075"/>
+    </listOfParameters>
+    <listOfConstraints>
+      <constraint metaid="c0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <ci> F </ci>
+            <apply>
+              <leq/>
+              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+              <cn type="integer"> 2100 </cn>
+            </apply>
+            <apply>
+              <and/>
+              <apply>
+                <gt/>
+                <ci> Z </ci>
+                <cn type="integer"> 80 </cn>
+              </apply>
+              <apply>
+                <lt/>
+                <ci> Y </ci>
+                <cn type="integer"> 40 </cn>
+              </apply>
+            </apply>
+          </apply>
+        </math>
+            </constraint>
+    </listOfConstraints>
+    <listOfReactions>
+      <reaction compartment="Cell" id="Production_P8" metaid="iBioSim27" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="FF" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="E"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P8 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> E </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P1" metaid="iBioSim14" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="D" stoichiometry="10"/>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P1 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> A </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P2" metaid="iBioSim16" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="E" stoichiometry="10"/>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P2 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> B </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P3" metaid="iBioSim18" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P3 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> X </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P4" metaid="iBioSim20" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="FF"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P4 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> FF </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P5" metaid="iBioSim22" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="C" stoichiometry="10"/>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P5 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> Z </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P6" metaid="iBioSim24" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P6 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> Y </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Production_P7" metaid="iBioSim26" reversible="false" sboTerm="SBO:0000589">
+        <listOfProducts>
+          <speciesReference constant="true" species="FF" stoichiometry="10"/>
+        </listOfProducts>
+        <listOfModifiers>
+          <modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
+          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
+        </listOfModifiers>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <apply>
+                  <divide/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <times/>
+                      <ci> P7 </ci>
+                      <ci> ko </ci>
+                    </apply>
+                    <ci> ko_f </ci>
+                  </apply>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <apply>
+                  <plus/>
+                  <cn type="integer"> 1 </cn>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> D </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_E" metaid="iBioSim43" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="E" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> E </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_C" metaid="iBioSim44" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="C" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> C </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_X" metaid="iBioSim45" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="X" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> X </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_D" metaid="iBioSim46" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="D" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> D </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_FF" metaid="iBioSim47" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="FF" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> FF </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_Y" metaid="iBioSim48" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="Y" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> Y </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+      <reaction compartment="Cell" id="Degradation_Z" metaid="iBioSim49" reversible="false">
+        <listOfReactants>
+          <speciesReference constant="true" species="Z" stoichiometry="10"/>
+        </listOfReactants>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> Z </ci>
+            </apply>
+          </math>
+                </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
diff --git a/prismtest/pro.csl b/prismtest/pro.csl
new file mode 100644
index 000000000..e86fc37d7
--- /dev/null
+++ b/prismtest/pro.csl
@@ -0,0 +1,10 @@
+
+// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
+
+P=? [ true U[0,1000] (YFP_protein >= 30) ]
+
+//P=? [ true U[0,1000] (YFP_protein > 30) ]
+
+//  // For 010to111 and 100to111
+// P=? [!(true U[0,1000] (YFP_protein > 30)) ]
+
diff --git a/prismtest/results.txt b/prismtest/results.txt
new file mode 100644
index 000000000..7ec12848e
--- /dev/null
+++ b/prismtest/results.txt
@@ -0,0 +1,2 @@
+0.0
+0.9997151321743104