Merge pull request #643 from MyersResearchGroup/fixModelGen

Fix issues with model generation libraries

README.md

@@ -24,9 +24,9 @@ biology.
 ##### Video Demo: [Tools Workflow](https://www.youtube.com/watch?v=g4xayzlyC2Q)
 ##### Contact: Chris Myers (@cjmyers) myers@ece.utah.edu
 
-Contributor(s): Nathan Barker, Pedro Fontanarrosa, Scott Glass, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam Nguyen, Tramy Nguyen, Tyler Patterson, Nicholas Roehner, Jason Stevens, Leandro Watanabe, Michael Zhang, Zhen Zhang, and Zach Zundel.
+Contributor(s): Nathan Barker, Lukas Buecherl, Pedro Fontanarrosa, Scott Glass, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam Nguyen, Tramy Nguyen, Tyler Patterson, Nicholas Roehner, Jason Stevens, Leandro Watanabe, Michael Zhang, Zhen Zhang, and Zach Zundel.
 
-Active Developer(s): Pedro Fontanarrosa, Chris Myers, Tramy Nguyen, Leandro Watanabe.
+Active Developer(s): Lukas Buecherl, Pedro Fontanarrosa, Chris Myers.
 
 ## Running iBioSim
 1. Download the iBioSim tool from the release page [here](https://github.com/MyersResearchGroup/iBioSim/releases):

analysis/log4j2.xml

@@ -1,65 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="WARN" name="XMLConfigTest" packages="org.sbml.*">
-  <Properties>
-    <Property name="filename">jsbml.log</Property>
-  </Properties>
-  <ThresholdFilter level="trace"/>
- 
-  <Appenders>
-    <Console name="console">
-      <PatternLayout pattern="%5p (%F:%L) - %m%n"/>
-    </Console>
-    <File name="file" fileName="${filename}">
-      <PatternLayout>
-        <pattern>%d %p %C{1.} [%t] %m%n</pattern>
-      </PatternLayout>
-    </File>
-  </Appenders>
- 
-  <Loggers>
-    <Logger name="org.sbml" level="info" additivity="false">
-      <AppenderRef ref="console"/>
-      <AppenderRef ref="file"/>
-    </Logger>
-
-<!--
-    <Logger name="org.sbml.jsbml.xml.stax.SBMLWriter" level="debug" additivity="false">
-      <AppenderRef ref="console"/>
-      <AppenderRef ref="file"/>      
-    </Logger>
-    
-    <Logger name="org.sbml.jsbml.xml.stax.SBMLReader" level="debug" additivity="false">
-      <AppenderRef ref="console"/>
-      <AppenderRef ref="file"/>      
-    </Logger>
--->
-<!--    
-# org.sbml.jsbml.test.SimpleSBaseChangeListener - DEBUG : it will display all add, remove or change event (lot of output when reading an SBML file)
-# org.sbml.jsbml.xml.parsers.SBMLCoreParser - ERROR to DEBUG : anything related to problems when parsing the SBML core elements.
-# org.sbml.jsbml.xml.parsers.StringParser - ERROR to DEBUG : (lot of output) display all the event when reading XHTML
-# org.sbml.jsbml.xml.parsers.AnnotationParser - DEBUG : output when reading non RDF annotations.
-# org.sbml.jsbml.xml.parsers.XMLNodeWriter - DEBUG : output events when writing XMLNode, so HTML block
-# org.sbml.jsbml.xml.stax.SBMLReader - ERROR to DEBUG : (lot of output) display all the event when reading an SBML file
-# org.sbml.jsbml.xml.stax.SBMLWriter - ERROR to DEBUG : (lot of output) display all the event when writing an SBML file
-# org.sbml.jsbml.util.StringTools - WARN : warning when there is a problem with the conversion of a String into a number or boolean.
-# org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler - WARN to DEBUG : (lot of output) display all the event when writing mathML
-# org.sbml.jsbml.xml.parsers.MathMLStaxParser - ERROR to DEBUG : (lot of output) display all the event when reading a MathML block
-# org.sbml.jsbml.SBMLDocument - ERROR to DEBUG : will display problems related to the checkConsistency call
-# org.sbml.jsbml.validator.SBMLValidator - DEBUG : will print the xml result file from http://sbml.org/validator/ with few others checks when the parsing is done
-# org.sbml.jsbml.util.SubModel - DEBUG : will print the details of the submodel building
-# org.sbml.jsbml.ASTNode - ERROR to DEBUG
-# org.sbml.jsbml.xml.parsers.AbstractReaderWriter - DEBUG : events when reading or writing L3 packages block (if the parser extends this abstract class)
-# org.sbml.jsbml.xml.parsers.QualParser - DEBUG : events when reading/writing the qual package/extension.
-# org.sbml.jsbml.ext.comp.CompModelPlugin - DEBUG: register and unregister debug output for the comp package id namespace
-# org.sbml.jsbml.ext.comp.ArraysSBasePlugin - DEBUG: register and unregister debug output for the arrays package id namespace
-# org.sbml.jsbml.Model - DEBUG: register and unregister debug output for the core package id namespace
-# org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser - DEBUG: debug output when reading and writing RDF annotations
-
-    
---> 
-    <Root level="info">
-      <AppenderRef ref="file"/>
-    </Root>
-  </Loggers>
- 
-</Configuration>

analysis/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>

analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Analysis.java

@@ -412,6 +412,7 @@ public class Analysis implements BioObserver
       if (modelSource.indexOf("/")!=-1) {
         modelSource = modelSource.substring(modelSource.lastIndexOf("/")+1);
       }
+      System.out.println("Reading: " + root + File.separator + modelSource);
       SBMLDocument sbmlDoc = SBMLReader.read(new File(root + File.separator + modelSource));
       if (model.getListOfChanges().size() != 0) {
         try {

analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/properties/PropertiesUtil.java

@@ -47,6 +47,17 @@ public class PropertiesUtil {
 				algorithm = new Algorithm(GlobalConstants.KISAO_EULER);
 			} else if (sim.contains("rk8pd")) {
 				algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_PRINCE_DORMAND);
+			} else if (sim.contains("rk4imp")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_IMPLICIT);
+			} else if (sim.contains("gear1")||sim.contains("gear2")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_GEAR);
+				AlgorithmParameter order;
+				if (sim.contains("gear1")) {
+					order = new AlgorithmParameter(GlobalConstants.KISAO_ORDER, "1");
+				} else {
+					order = new AlgorithmParameter(GlobalConstants.KISAO_ORDER, "2");
+				}
+				algorithm.addAlgorithmParameter(order);
 			} else if (sim.contains("rkf45") || sim.contains("Runge-Kutta-Fehlberg")) {
 				algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_FEHLBERG);
 				para.setAttribute("method", sim);
@@ -57,6 +68,10 @@ public class PropertiesUtil {
 		} else if (properties.isSsa()) {
 			if (sim.equals("gillespie")) {
 				algorithm = new Algorithm(GlobalConstants.KISAO_GILLESPIE_DIRECT);
+			} else if (sim.equals("bunker")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_BUNKER);
+			} else if (sim.equals("emc")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_EMC);
 			}
 
 			else if (sim.contains("Mixed")) {
@@ -146,6 +161,12 @@ public class PropertiesUtil {
 		} else if (kisaoId.equals(GlobalConstants.KISAO_RUNGE_KUTTA_PRINCE_DORMAND)) {
 			properties.setOde();
 			properties.setSim("rk8pd");
+		} else if (kisaoId.equals(GlobalConstants.KISAO_BUNKER)) {
+			properties.setOde();
+			properties.setSim("bunker");
+		} else if (kisaoId.equals(GlobalConstants.KISAO_EMC)) {
+			properties.setOde();
+			properties.setSim("emc");
 		} else if (kisaoId.equals(GlobalConstants.KISAO_GILLESPIE) || kisaoId.equals(GlobalConstants.KISAO_GILLESPIE_DIRECT)) {
 			properties.setSsa();
 			properties.setSim("gillespie");

bin/iBioSim.mac64

@@ -8,4 +8,4 @@ export PATH=$BIOSIM/bin:/usr/local/lib:$PATH
 export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH
 export DDLD_LIBRARY_PATH=/usr/local/lib:$DDLD_LIBRARY_PATH
 
-exec java -Xmx2048M -Xms2048M -Djava.library.path=/usr/local/lib -XX:+UseSerialGC -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/src/main/resources/edu/utah/ece/async/ibiosim/gui/icons/iBioSim.jpg -jar iBioSim.jar 
+java --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx2048M -Xms2048M -Djava.library.path=/usr/local/lib -XX:+UseSerialGC -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/src/main/resources/edu/utah/ece/async/ibiosim/gui/icons/iBioSim.jpg -jar iBioSim.jar 

conversion/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>
@@ -62,13 +62,15 @@
 		</dependency>	
 		<dependency>
 			<groupId>org.apache.jena</groupId>
-			<artifactId>jena-base</artifactId>
+			<artifactId>apache-jena-libs</artifactId>
 			<version>3.0.0</version>
+			<type>pom</type>
+			<scope>import</scope>
 		</dependency>
 		<dependency>
-			<groupId>org.apache.jena</groupId>
-			<artifactId>jena-arq</artifactId>
-			<version>3.0.0</version>
+  			<groupId>xerces</groupId>
+ 			 <artifactId>xercesImpl</artifactId>
+  			<version>2.12.2</version>
 		</dependency>
 	</dependencies>
 	 <repositories>

conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java

@@ -77,7 +77,6 @@ public class Converter {
 				+ "and can convert to/from SBOL 1.1, to/from SBML, GenBank, and FASTA formats.");
 		System.err.println();
 		System.err.println("Usage:");
-		//TODO PEDRO shouldnt this be conersion 3.0.0-SNAPSHOT?
 		System.err.println("\tjava -jar iBioSim-conversion-0.0.1-SNAPSHOT-jar-with-dependencies.jar [options] inputFile ");
 		System.err.println();
 		System.err.println("Convert SBOL to SBML Example:");
@@ -554,6 +553,7 @@ public class Converter {
 						SBOLDocument sbolDoc = SBOLUtility.loadSBOLFile(fullInputFileName, URIPrefix);
 						String circuit_name = file.getName();
 						circuit_name = circuit_name.replace(".xml", "");
+						circuit_name = circuit_name.replace(".sbol", "");
 						String vpr_output =  circuit_name + "_topModule";
 
 						if(!topLevelURIStr.isEmpty())
@@ -610,9 +610,8 @@ public class Converter {
 								SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
 							} 
 						}
-
 						if (topModelId != null) {
-							SBMLDocument topModel = SBMLutilities.readSBML(vpr_output+".xml", null, null);
+							SBMLDocument topModel = SBMLutilities.readSBML(outputDir + File.separator + vpr_output+ ".xml", null, null);
 							topModel.getModel().setId(topModelId);
 							SBMLWriter writer = new SBMLWriter();
 							try {
@@ -629,7 +628,6 @@ public class Converter {
 								e.printStackTrace();
 							}
 						}
-
 						if (doVPR) {
 							if (topEnvir) {
 								SBMLDocument topEnvironment = SBMLutilities.readSBML(environment, null, null);

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 {
@@ -73,161 +74,340 @@ 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");
 
 		}
 
@@ -237,17 +417,13 @@ public class SBML2PRISM {
 
 	}
 
-	
 	/*
-	 * 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));
 			}
 
 		}

dataModels/pom.xml

@@ -16,21 +16,11 @@
 			<name>The JSBML Snapshot repository</name>
 			<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
 		</repository>
-		<repository>
-			<id>ebi</id>
-			<name>ebi</name>
-			<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
-		</repository>
-		<repository>
+			<repository>
 			<id>jboss</id>
 			<name>jboss</name>
 			<url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
 		</repository>
-		<repository>
-			<id>netbeans</id>
-			<name>netbeans</name>
-			<url>http://bits.netbeans.org/maven2/</url>
-		</repository>
 		<repository>
 			<id>osgeo</id>
 			<name>osgeo</name>
@@ -54,8 +44,26 @@
 			<groupId>jaxen</groupId>
 			<artifactId>jaxen</artifactId>
 			<version>1.1.4</version>
+			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>xom</groupId>
+                	<artifactId>xom</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>dom4j</groupId>
+                	<artifactId>dom4j</artifactId>
+            	</exclusion>
+        	</exclusions>
 		</dependency>
-
+		
 		<dependency>
 			<groupId>xom</groupId>
 			<artifactId>xom</artifactId>
@@ -71,7 +79,7 @@
 		<dependency>
 			<groupId>org.sbml.jsbml</groupId>
 			<artifactId>jsbml</artifactId>
-			<version>1.6-SNAPSHOT</version>
+			<version>1.7-SNAPSHOT</version>
 		</dependency>
 
 		<dependency>
@@ -85,6 +93,20 @@
 			<groupId>org.sbolstandard</groupId>
 			<artifactId>libSBOLj</artifactId>
 			<version>2.4.1-SNAPSHOT</version>
+			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>dom4j</groupId>
+                	<artifactId>dom4j</artifactId>
+            	</exclusion>
+        	</exclusions>			
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
@@ -98,17 +120,56 @@
 			<groupId>org.jfree</groupId>
 			<artifactId>jfreechart</artifactId>
 			<version>1.0.14</version>
+			<exclusions>
+			   <exclusion>
+             	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	   </exclusion>
+           	    <exclusion>
+             	   <groupId>xml-apis</groupId>
+                   <artifactId>xml-apis-ext</artifactId>
+           	    </exclusion>
+       		    <exclusion>
+           			 <groupId>xerces</groupId>
+            		 <artifactId>xercesImpl</artifactId>
+        		</exclusion>
+           	</exclusions>
 		</dependency>
-				<dependency>
+		
+		<dependency>
 			<groupId>org.apache.xmlgraphics</groupId>
 			<artifactId>batik-dom</artifactId>
-			<version>1.8</version>
+			<version>1.16</version>
+			<exclusions>
+        		<exclusion>
+            		<groupId>xml-apis</groupId>
+            		<artifactId>xml-apis</artifactId>
+       			</exclusion>
+			       <exclusion>
+             	   <groupId>xml-apis</groupId>
+                   <artifactId>xml-apis-ext</artifactId>
+           	    </exclusion>
+       			<exclusion>
+           			 <groupId>xerces</groupId>
+            		 <artifactId>xercesImpl</artifactId>
+        		</exclusion>
+   			</exclusions>			
 		</dependency>
 
 		<dependency>
 			<groupId>org.apache.xmlgraphics</groupId>
 			<artifactId>batik-svggen</artifactId>
-			<version>1.8</version>
+			<version>1.16</version>
+			<exclusions>
+        		<exclusion>
+            		<groupId>xml-apis</groupId>
+            		<artifactId>xml-apis</artifactId>
+       			</exclusion>
+       			<exclusion>
+           			 <groupId>xerces</groupId>
+            		 <artifactId>xercesImpl</artifactId>
+        		</exclusion>
+   			</exclusions>
 		</dependency>
 		
 		<dependency>
@@ -122,11 +183,29 @@
    			<artifactId>VectorGraphics2D</artifactId>
     		<version>0.13</version>
 		</dependency>
-		
+
 		<dependency>
             <groupId>org.jlibsedml</groupId>
             <artifactId>jlibsedml</artifactId>
             <version>2.3.0-SNAPSHOT</version>
+            			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>xom</groupId>
+                	<artifactId>xom</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>jaxen</groupId>
+                	<artifactId>jaxen</artifactId>
+            	</exclusion>
+        	</exclusions>
         </dependency>
         	
 		<dependency>

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java

@@ -195,125 +195,125 @@ public class BioModel extends CoreObservable{
 	private void loadDefaultParameters() {
 		Preferences biosimrc = Preferences.userRoot();
 
-		createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_KREP_STRING, "1");
 		
-		createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_KACT_STRING, "1");
 
-		createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
 
 		createGlobalParameter(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING, 
-				biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
+				biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
 
-		createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
 
-		createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
-		createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
+		createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
 
-		createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
-		createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
-		createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
-		createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
-		createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
-		createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
+		createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
+		createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
+		createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
+		createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
+		createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
+		createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
+		createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
+		createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
+		createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
+		createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
 	}
 
 	private void loadDefaultParameterMap() {
 		Preferences biosimrc = Preferences.userRoot();
 		defaultParameters = new HashMap<String,String>();
 
-		defaultParameters.put(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
+		defaultParameters.put(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
 		defaultParameters.put(GlobalConstants.REVERSE_KREP_STRING, "1");
 		
-		defaultParameters.put(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
+		defaultParameters.put(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
 		defaultParameters.put(GlobalConstants.REVERSE_KACT_STRING, "1");
 
-		defaultParameters.put(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
+		defaultParameters.put(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
 		defaultParameters.put(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
 
 		defaultParameters.put(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING, 
-				biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
+				biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
 		defaultParameters.put(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
 
-		defaultParameters.put(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
+		defaultParameters.put(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
 		defaultParameters.put(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
 
-		defaultParameters.put(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
-		defaultParameters.put(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
+		defaultParameters.put(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
+		defaultParameters.put(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
 
-		defaultParameters.put(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
-		defaultParameters.put(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
-		defaultParameters.put(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
-		defaultParameters.put(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
-		defaultParameters.put(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
-		defaultParameters.put(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
-		defaultParameters.put(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
-		defaultParameters.put(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
-		defaultParameters.put(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
-		defaultParameters.put(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
+		defaultParameters.put(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
+		defaultParameters.put(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
+		defaultParameters.put(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
+		defaultParameters.put(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
+		defaultParameters.put(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
+		defaultParameters.put(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
+		defaultParameters.put(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
+		defaultParameters.put(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
+		defaultParameters.put(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
+		defaultParameters.put(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
 	}
 
 	private void createDegradationDefaultParameters() {
 		Preferences biosimrc = Preferences.userRoot();
 
-		createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", ""));
+		createGlobalParameter(GlobalConstants.KDECAY_STRING, biosimrc.get("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE));
 	}
 
 	private void createDiffusionDefaultParameters() {
 		Preferences biosimrc = Preferences.userRoot();
 
-		createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", ""));
-		createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", ""));
-		createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_MEMDIFF_STRING, biosimrc.get("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE));
+		createGlobalParameter(GlobalConstants.REVERSE_MEMDIFF_STRING, biosimrc.get("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE));
+		createGlobalParameter(GlobalConstants.KECDECAY_STRING, biosimrc.get("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE));
+		createGlobalParameter(GlobalConstants.KECDIFF_STRING, biosimrc.get("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE));
 	}
 
 	private void createComplexDefaultParameters() {
 		Preferences biosimrc = Preferences.userRoot();
 
-		createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_KCOMPLEX_STRING, biosimrc.get("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_KCOMPLEX_STRING, "1");
-		createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
+		createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
 	}
 
 	private void createConstitutiveDefaultParameters() {
 		Preferences biosimrc = Preferences.userRoot();
 
-		createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
+		createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
+		createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
 	}
 	
 	private void createProductionDefaultParameters() {
 		Preferences biosimrc = Preferences.userRoot();
 
-		createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_KREP_STRING, biosimrc.get("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_KREP_STRING, "1");
 		
-		createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_KACT_STRING, biosimrc.get("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_KACT_STRING, "1");
 
-		createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", ""));
+		createGlobalParameter(GlobalConstants.FORWARD_RNAP_BINDING_STRING, biosimrc.get("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_RNAP_BINDING_STRING, "1");
 
 		createGlobalParameter(GlobalConstants.FORWARD_ACTIVATED_RNAP_BINDING_STRING, 
-				biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", ""));
+				biosimrc.get("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE));
 		createGlobalParameter(GlobalConstants.REVERSE_ACTIVATED_RNAP_BINDING_STRING, "1");
 
-		createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", ""));
-		createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", ""));
-		createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", ""));
-		createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", ""));
-		createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", ""));
-		createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", ""));
+		createGlobalParameter(GlobalConstants.COOPERATIVITY_STRING, biosimrc.get("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE));
+		createGlobalParameter(GlobalConstants.RNAP_STRING, biosimrc.get("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE));
+		createGlobalParameter(GlobalConstants.OCR_STRING, biosimrc.get("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE));
+		createGlobalParameter(GlobalConstants.KBASAL_STRING, biosimrc.get("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE));
+		createGlobalParameter(GlobalConstants.PROMOTER_COUNT_STRING, biosimrc.get("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE));
+		createGlobalParameter(GlobalConstants.STOICHIOMETRY_STRING, biosimrc.get("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE));
+		createGlobalParameter(GlobalConstants.ACTIVATED_STRING, biosimrc.get("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE));
 	}
 	
 	public static boolean IsDefaultParameter(String paramId) {

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java

@@ -461,6 +461,7 @@ public class SBMLutilities extends CoreObservable
 	}
 	
 	public static void copyDimensionsToEdgeIndex(SBase source,SBase target,SBase edge,String attribute) {
+		if (source==null || target==null) return;
 		if (SBMLutilities.dimensionsMatch(source,target)) {
 			ArraysSBasePlugin sBasePlugin = SBMLutilities.getArraysSBasePlugin(source);
 			ArraysSBasePlugin sBasePluginEdge = SBMLutilities.getArraysSBasePlugin(edge);

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/graphData/GraphData.java

@@ -19,8 +19,6 @@ import java.util.Scanner;
 
 import javax.swing.JComboBox;
 
-import org.apache.batik.dom.GenericDOMImplementation;
-import org.apache.batik.svggen.SVGGraphics2D;
 import org.jfree.chart.ChartFactory;
 import org.jfree.chart.ChartUtilities;
 import org.jfree.chart.JFreeChart;
@@ -53,7 +51,8 @@ import org.jlibsedml.SEDMLDocument;
 import org.jlibsedml.SedML;
 import org.jlibsedml.Variable;
 import org.jlibsedml.modelsupport.SBMLSupport;
-import org.w3c.dom.DOMImplementation;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.batik.dom.GenericDOMImplementation;
 
 import com.lowagie.text.Document;
 import com.lowagie.text.Rectangle;
@@ -301,6 +300,7 @@ public class GraphData extends CoreObservable {
 			doc.writeTo(new FileOutputStream(file));
 		}
 		else if (output == 4) {
+			/*
 			DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
 			org.w3c.dom.Document document = domImpl.createDocument(null, "svg", null);
 			SVGGraphics2D svgGenerator = new SVGGraphics2D(document);
@@ -311,6 +311,7 @@ public class GraphData extends CoreObservable {
 			svgGenerator.stream(out, useCSS);
 			out.close();
 			outStream.close();
+			*/
 		}
 		else if ((output == 5) || (output == 6) || (output == 7)) {
 			exportDataFile(file, output);

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/GlobalConstants.java

@@ -72,19 +72,25 @@ public class GlobalConstants {
 	public static final String TRANSCRIPTION_FACTOR = "transcription factor";
 
 	
-//	public static final String KREP_VALUE = ".5"; 
-//	public static final String KACT_VALUE = ".0033";
-//	public static final String KBIO_VALUE = ".05";
-//	public static final String PROMOTER_COUNT_VALUE = "2";
-//	public static final String KASSOCIATION_VALUE = ".05";
-//	public static final String KBASAL_VALUE = ".0001";
-//	public static final String OCR_VALUE = ".05";
-//	public static final String KDECAY_VALUE = ".0075";
-//	public static final String RNAP_VALUE = "30";
-//	public static final String RNAP_BINDING_VALUE = ".033";
-//	public static final String STOICHIOMETRY_VALUE = "10";
-//	public static final String COOPERATIVITY_VALUE = "2";
-//	public static final String ACTIVED_VALUE = ".25";
+	public static final String KREP_VALUE = ".5"; 
+	public static final String KACT_VALUE = ".0033";
+	public static final String KBIO_VALUE = ".05";
+	public static final String PROMOTER_COUNT_VALUE = "2";
+	public static final String KASSOCIATION_VALUE = ".05";
+	public static final String KBASAL_VALUE = ".0001";
+	public static final String OCR_VALUE = ".05";
+	public static final String KDECAY_VALUE = ".0075";
+	public static final String KECDECAY_VALUE = ".005";
+	public static final String KCOMPLEX_VALUE = ".05";
+	public static final String RNAP_VALUE = "30";
+	public static final String RNAP_BINDING_VALUE = ".033";
+	public static final String STOICHIOMETRY_VALUE = "10";
+	public static final String COOPERATIVITY_VALUE = "2";
+	public static final String ACTIVED_VALUE = ".25";
+	public static final String ACTIVATED_RNAP_BINDING_VALUE = "1";
+	public static final String FORWARD_MEMDIFF_VALUE = "1";
+	public static final String REVERSE_MEMDIFF_VALUE = ".01";
+	public static final String KECDIFF_VALUE = "1.0";
 	
 	public static final String ID = "ID";
 	public static final String COMPONENT = "Component";
@@ -290,22 +296,27 @@ public class GlobalConstants {
 	public static final String KISAO_GILLESPIE = "KISAO:0000241";
 	public static final String KISAO_GILLESPIE_DIRECT = "KISAO:0000029";
 	public static final String KISAO_SSA_CR = "KISAO:0000329";
+	public static final String KISAO_BUNKER = "KISAO:0000618";
+	public static final String KISAO_EMC = "KISAO:0000619";
 	public static final String KISAO_EULER = "KISAO:0000030";
+	public static final String KISAO_GEAR = "KISAO:0000288";
 	public static final String KISAO_RUNGE_KUTTA_FEHLBERG = "KISAO:0000086";
-	public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000087";
+	public static final String KISAO_RUNGE_KUTTA_IMPLICIT = "KISAO:0000612";
+	public static final String KISAO_RUNGE_KUTTA_PRINCE_DORMAND = "KISAO:0000609";
 	public static final String KISAO_LSODA = "KISAO:0000088";
 	public static final String KISAO_FBA = "KISAO:0000437";
 	public static final String KISAO_MINIMUM_STEP_SIZE = "KISAO:0000485";
 	public static final String KISAO_MAXIMUM_STEP_SIZE = "KISAO:0000467";
 	public static final String KISAO_ABSOLUTE_TOLERANCE = "KISAO:0000211";
 	public static final String KISAO_RELATIVE_TOLERANCE = "KISAO:0000209";
+	public static final String KISAO_ORDER = "KISAO:0000594";
 	public static final String KISAO_SEED = "KISAO:0000488";
 	public static final String KISAO_SAMPLES = "KISAO:0000326";
 	public static final String KISAO_NUMBER_OF_RUNS = "KISAO:0000498";
 	public static final String KISAO_DFBA = "KISAO_0000499";
 	public static final String KISAO_DFBA_SOA = "KISAO:0000500";
-	public static final String KISAO_DFBA_DOA = "KISAO:0000501 ";
-	public static final String KISAO_DFBA_DA = "KISAO:0000501 ";
+	public static final String KISAO_DFBA_DOA = "KISAO:0000501";
+	public static final String KISAO_DFBA_DA = "KISAO:0000501";
 	
 	public static final String TRUE = "true";
 	public static final String FALSE = "false";

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/IBioSimPreferences.java

@@ -282,55 +282,55 @@ public enum IBioSimPreferences {
 			modelPreferences.put(modelPreference, Preferences.userRoot().get(modelPreference, ""));
 			if (modelPreferences.get(modelPreference).equals("")) {
 				if (modelPreference.equals("biosim.gcm.KREP_VALUE")) {
-					modelPreferences.put("biosim.gcm.KREP_VALUE", ".5");
+					modelPreferences.put("biosim.gcm.KREP_VALUE", GlobalConstants.KREP_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.KACT_VALUE")) {
-					modelPreferences.put("biosim.gcm.KACT_VALUE", ".0033");
+					modelPreferences.put("biosim.gcm.KACT_VALUE", GlobalConstants.KACT_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.PROMOTER_COUNT_VALUE")) {
-					modelPreferences.put("biosim.gcm.PROMOTER_COUNT_VALUE", "2");
+					modelPreferences.put("biosim.gcm.PROMOTER_COUNT_VALUE", GlobalConstants.PROMOTER_COUNT_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.KBASAL_VALUE")) {
-					modelPreferences.put("biosim.gcm.KBASAL_VALUE", ".0001");
+					modelPreferences.put("biosim.gcm.KBASAL_VALUE", GlobalConstants.KBASAL_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.OCR_VALUE")) {
-					modelPreferences.put("biosim.gcm.OCR_VALUE", ".05");
+					modelPreferences.put("biosim.gcm.OCR_VALUE", GlobalConstants.OCR_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.KDECAY_VALUE")) {
-					modelPreferences.put("biosim.gcm.KDECAY_VALUE", ".0075");
+					modelPreferences.put("biosim.gcm.KDECAY_VALUE", GlobalConstants.KDECAY_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.KECDECAY_VALUE")) {
-					modelPreferences.put("biosim.gcm.KECDECAY_VALUE", ".005");
+					modelPreferences.put("biosim.gcm.KECDECAY_VALUE", GlobalConstants.KECDECAY_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.RNAP_VALUE")) {
-					modelPreferences.put("biosim.gcm.RNAP_VALUE", "30");
+					modelPreferences.put("biosim.gcm.RNAP_VALUE", GlobalConstants.RNAP_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.RNAP_BINDING_VALUE")) {
-					modelPreferences.put("biosim.gcm.RNAP_BINDING_VALUE", ".033");
+					modelPreferences.put("biosim.gcm.RNAP_BINDING_VALUE", GlobalConstants.RNAP_BINDING_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE")) {
-					modelPreferences.put("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", "1");
+					modelPreferences.put("biosim.gcm.ACTIVATED_RNAP_BINDING_VALUE", GlobalConstants.ACTIVATED_RNAP_BINDING_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.STOICHIOMETRY_VALUE")) {
-					modelPreferences.put("biosim.gcm.STOICHIOMETRY_VALUE", "10");
+					modelPreferences.put("biosim.gcm.STOICHIOMETRY_VALUE", GlobalConstants.STOICHIOMETRY_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.KCOMPLEX_VALUE")) {
-					modelPreferences.put("biosim.gcm.KCOMPLEX_VALUE", "0.05");
+					modelPreferences.put("biosim.gcm.KCOMPLEX_VALUE", GlobalConstants.KCOMPLEX_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.COOPERATIVITY_VALUE")) {
-					modelPreferences.put("biosim.gcm.COOPERATIVITY_VALUE", "2");
+					modelPreferences.put("biosim.gcm.COOPERATIVITY_VALUE", GlobalConstants.COOPERATIVITY_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.ACTIVED_VALUE")) {
-					modelPreferences.put("biosim.gcm.ACTIVED_VALUE", ".25");
+					modelPreferences.put("biosim.gcm.ACTIVED_VALUE", GlobalConstants.ACTIVED_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.FORWARD_MEMDIFF_VALUE")) {
-					modelPreferences.put("biosim.gcm.FORWARD_MEMDIFF_VALUE", "1.0");
+					modelPreferences.put("biosim.gcm.FORWARD_MEMDIFF_VALUE", GlobalConstants.FORWARD_MEMDIFF_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.REVERSE_MEMDIFF_VALUE")) {
-					modelPreferences.put("biosim.gcm.REVERSE_MEMDIFF_VALUE", "0.01");
+					modelPreferences.put("biosim.gcm.REVERSE_MEMDIFF_VALUE", GlobalConstants.REVERSE_MEMDIFF_VALUE);
 				}
 				if (modelPreference.equals("biosim.gcm.KECDIFF_VALUE")) {
-					modelPreferences.put("biosim.gcm.KECDIFF_VALUE", "1.0");
+					modelPreferences.put("biosim.gcm.KECDIFF_VALUE", GlobalConstants.KECDIFF_VALUE);
 				}
 			}
 		}

gui/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>
@@ -38,31 +38,16 @@
 		</plugins>
 	</build>
     <repositories>
-         <repository>
-            <id>staging</id>
-            <name>staging</name>
-            <url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url>
-        </repository>
         <repository>
             <id>ossrh</id>
             <name>ossrh</name>
             <url>https://oss.sonatype.org/content/repositories/snapshots</url>
         </repository>
-        <repository>
-			<id>ebi</id>
-			<name>ebi</name>
-			<url>https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
-		</repository>
 		<repository>
 			<id>jboss</id>
 			<name>jboss</name>
 			<url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
 		</repository>
-		<repository>
-			<id>netbeans</id>
-			<name>netbeans</name>
-			<url>https://bits.netbeans.org/maven2/</url>
-		</repository>
 		<repository>
 			<id>osgeo</id>
 			<name>osgeo</name>
@@ -92,6 +77,20 @@
 			<groupId>org.jfree</groupId>
 			<artifactId>jfreechart</artifactId>
 			<version>1.0.14</version>
+			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>dom4j</groupId>
+                	<artifactId>dom4j</artifactId>
+            	</exclusion>
+        	</exclusions>
 		</dependency>
 
 		<dependency>
@@ -179,6 +178,12 @@
     		<artifactId>jdom2</artifactId>
     		<version>2.0.6</version>
 		</dependency>
+		
+		<dependency>
+  			<groupId>xerces</groupId>
+ 			 <artifactId>xercesImpl</artifactId>
+  			<version>2.12.2</version>
+		</dependency>
 
 	</dependencies>
 </project>

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java

@@ -36,6 +36,8 @@ import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.awt.event.WindowEvent;
 import java.awt.event.WindowListener;
+import java.awt.Desktop;
+
 import java.io.BufferedReader;
 import java.io.BufferedWriter;
 import java.io.ByteArrayOutputStream;
@@ -210,7 +212,6 @@ import edu.utah.ece.async.ibiosim.gui.synthesisView.SynthesisView;
 import edu.utah.ece.async.ibiosim.gui.synthesisView.SynthesisViewATACS;
 import edu.utah.ece.async.ibiosim.gui.util.FileTree;
 import edu.utah.ece.async.ibiosim.gui.util.Log;
-import edu.utah.ece.async.ibiosim.gui.util.OSXHandlers;
 import edu.utah.ece.async.ibiosim.gui.util.Utility;
 import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
 import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog;
@@ -334,7 +335,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 
 	public static Object ICON_COLLAPSE = UIManager.get("Tree.collapsedIcon");
 
-	protected static final String		iBioSimVersion		= "3.1.0";	
+	protected static final String		iBioSimVersion		= "3.2.0";	
 
 	protected SEDMLDocument 			sedmlDocument		= null;
 
@@ -882,9 +883,38 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		
 		help.add(manual);
 		help.add(bugReport);
-		if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
-			OSXHandlers osxHandlers = new OSXHandlers(this);
-			osxHandlers.addEventHandlers();
+		if (Desktop.isDesktopSupported()) {
+            Desktop desktop = Desktop.getDesktop();
+
+            if (desktop.isSupported(Desktop.Action.APP_ABOUT)) {
+            	// Set the "About" menu handler
+            	desktop.setAboutHandler(e -> {
+            		about();
+            	});
+            }
+
+            if (desktop.isSupported(Desktop.Action.APP_PREFERENCES)) {
+            	// Set the "Preferences" menu handler
+            	desktop.setPreferencesHandler(e -> {
+            		PreferencesDialog.showPreferences(Gui.frame);
+            		getFileTree().setExpandibleIcons(!IBioSimPreferences.INSTANCE.isPlusMinusIconsEnabled());
+            		if (getSBOLDocument() != null) {
+            			getSBOLDocument().setDefaultURIprefix(SBOLEditorPreferences.INSTANCE.getUserInfo().getURI().toString());
+            		}
+            	});
+            }
+            
+            if (desktop.isSupported(Desktop.Action.APP_QUIT_HANDLER)) {
+            	// Set the "Quit" menu handler
+            	desktop.setQuitHandler((e, response) -> {
+            		exit();
+            		// If we have returned from the above call the user has decided not to quit
+            		response.cancelQuit();
+            		// Perform cleanup before exiting
+            		//response.performQuit(); // or response.cancelQuit();
+            	});
+            }
+            
 		} else {
 			edit.addSeparator();
 			edit.add(pref);
@@ -1040,7 +1070,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		final String developers;
 		name = new JLabel("iBioSim", SwingConstants.CENTER);
 		version = new JLabel("Version " + iBioSimVersion, SwingConstants.CENTER);
-		developers = "Nathan Barker\nScott Glass\nKevin Jones\nHiroyuki Kuwahara\n"
+		developers = "Nathan Barker\nLukas Buecherl\nPedro Fontanarrosa\nScott Glass\nKevin Jones\nHiroyuki Kuwahara\n"
 				+ "Curtis Madsen\nChris Myers\nNam Nguyen\nTramy Nguyen\nTyler Patterson\nNicholas Roehner\nJason Stevens\nLeandro Watanabe\nMichael Zhang\nZhen Zhang\nZach Zundel";
 		Font font = name.getFont();
 		font = font.deriveFont(Font.BOLD, 36.0f);
@@ -2407,7 +2437,12 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		} else if (e.getSource().equals(importArchive)) {
 			importArchive();
 		} else if (e.getSource().equals(downloadSynBioHub)) {
-			downloadSynBioHub();
+			try {
+				downloadSynBioHub();
+			} catch (SBOLValidationException e1) {
+				// TODO Auto-generated catch block
+				e1.printStackTrace();
+			}
 		} else if (e.getSource() == downloadBioModel) {
 			downloadBioModel();
 		} else if (e.getSource() == downloadVirtualPart) {
@@ -4524,7 +4559,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		}		
 	}
 	
-	public void createCombineArchive(File archiveFile, String filename) throws IOException, JDOMException, ParseException, CombineArchiveException, TransformerException {
+	public void createCombineArchive(File archiveFile, String filename) throws IOException, JDOMException, ParseException, CombineArchiveException {
 		CombineArchive archive = new CombineArchive(archiveFile);
 		File baseDir = new File(root);
 		if (filename == null) {
@@ -4534,7 +4569,11 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		} else {
 			addFileToCombineArchive(archive,baseDir,filename);
 		} 
-		archive.pack();
+		try {
+			archive.pack();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
 		archive.close();
 	}
 	
@@ -4569,8 +4608,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 					try {
 						createCombineArchive(file,null);
 					}
-					catch (IOException | JDOMException | ParseException | CombineArchiveException
-							| TransformerException e) {
+					catch (IOException | JDOMException | ParseException | CombineArchiveException e) {
 						JOptionPane.showMessageDialog(frame, "Unable to export COMBINE Archive file.", "Error",
 								JOptionPane.ERROR_MESSAGE);
 					}
@@ -4605,7 +4643,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		return null;
 	}
 	
-	public void downloadSynBioHub() {
+	public void downloadSynBioHub() throws SBOLValidationException {
 		RegistryInputDialog registryInputDialog = new RegistryInputDialog(Gui.frame, RegistryInputDialog.ALL_PARTS,
 				edu.utah.ece.async.sboldesigner.sbol.SBOLUtils.Types.All_types, null, sbolDocument);
 		registryInputDialog.allowCollectionSelection();
@@ -4638,7 +4676,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 				getSBOLDocument().createCopy(selection);
 				writeSBOLDocument();
 			}
-			catch (SBOLValidationException | SynBioHubException | IOException e) {
+			catch (SynBioHubException | IOException e) {
 				// TODO Auto-generated catch block
 				e.printStackTrace();
 				JOptionPane.showMessageDialog(frame, "Unable to download from SynBioHub.", "Error Exporting to SynBioHub",

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/movie/MovieContainer.java

@@ -819,9 +819,18 @@ public class MovieContainer extends PanelObservable implements ActionListener {
 	public void savePreferences() {
 
 		Gson gson = new Gson();
-		String out = gson.toJson(this.movieScheme.getAllSpeciesSchemes());
+		String out; 
+		String fullPath;
 		
-		String fullPath = getPreferencesFullPath();
+		try {
+			out = gson.toJson(this.movieScheme.getAllSpeciesSchemes());
+			fullPath = getPreferencesFullPath();
+		} 
+		catch (Exception e) {
+			e.printStackTrace();
+			JOptionPane.showMessageDialog(Gui.frame, "An error occured preparing to save movie preferences " + "\nmessage: " + e.getMessage());
+			return;
+		}
 		
 		FileOutputStream fHandle;
 		

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/schematic/BioGraph.java

@@ -209,10 +209,14 @@ public class BioGraph extends mxGraph {
 //		SBMLutilities.copyIndices(getGlyph(layout,GlobalConstants.GLYPH+"__"+product), speciesReferenceGlyph, "layout:speciesGlyph");
 //		SBMLutilities.copyIndices(reactionGlyph, speciesReferenceGlyph, "layout:id");
 		LineSegment lineSegment = speciesReferenceGlyph.createCurve().createLineSegment();
-		lineSegment.setStart(new Point(this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterX(),
-				this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterY()));
-		lineSegment.setEnd(new Point(this.getSpeciesOrPromoterCell(product).getGeometry().getCenterX(),
-				this.getSpeciesOrPromoterCell(product).getGeometry().getCenterY()));
+		if (this.getSpeciesOrPromoterCell(reactant)!=null) {
+			lineSegment.setStart(new Point(this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterX(),
+					this.getSpeciesOrPromoterCell(reactant).getGeometry().getCenterY()));
+		}
+		if (this.getSpeciesOrPromoterCell(product)!=null) {
+			lineSegment.setEnd(new Point(this.getSpeciesOrPromoterCell(product).getGeometry().getCenterX(),
+					this.getSpeciesOrPromoterCell(product).getGeometry().getCenterY()));
+		}
 	}
 
 	private static void addSpeciesReferenceGlyph(Layout layout,mxCell cell,ReactionGlyph reactionGlyph,String reactionId,String speciesId, String role) {
@@ -223,8 +227,12 @@ public class BioGraph extends mxGraph {
 //			SBMLutilities.copyIndices(getGlyph(layout,GlobalConstants.GLYPH+"__"+speciesId), speciesReferenceGlyph, "layout:speciesGlyph");
 //			SBMLutilities.copyIndices(reactionGlyph, speciesReferenceGlyph, "layout:id");
 			LineSegment lineSegment = speciesReferenceGlyph.createCurve().createLineSegment();
-			lineSegment.setStart(new Point(cell.getSource().getGeometry().getCenterX(),cell.getSource().getGeometry().getCenterY()));
-			lineSegment.setEnd(new Point(cell.getTarget().getGeometry().getCenterX(),cell.getTarget().getGeometry().getCenterY()));
+			if (cell.getSource()!=null) {
+				lineSegment.setStart(new Point(cell.getSource().getGeometry().getCenterX(),cell.getSource().getGeometry().getCenterY()));
+			}
+			if (cell.getTarget()!=null) {
+				lineSegment.setEnd(new Point(cell.getTarget().getGeometry().getCenterX(),cell.getTarget().getGeometry().getCenterY()));
+			}
 		}
 	}
 

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/util/OSXHandlers.java

@@ -1,104 +0,0 @@
-package edu.utah.ece.async.ibiosim.gui.util;
-
-import java.io.File;
-import java.lang.reflect.InvocationHandler;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.lang.reflect.Proxy;
-import java.util.List;
-
-import javax.swing.JFrame;
-
-import org.apache.commons.lang3.JavaVersion;
-
-import com.apple.eawt.AboutHandler;
-import com.apple.eawt.Application;
-import com.apple.eawt.PreferencesHandler;
-import com.apple.eawt.QuitHandler;
-import com.apple.eawt.QuitResponse;
-import com.apple.eawt.AppEvent.AboutEvent;
-import com.apple.eawt.AppEvent.PreferencesEvent;
-import com.apple.eawt.AppEvent.QuitEvent;
-
-import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
-import edu.utah.ece.async.ibiosim.gui.Gui;
-import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog;
-import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLEditorPreferences;
-
-public class OSXHandlers implements InvocationHandler {
-	
-	Gui gui;
-			
-	public OSXHandlers(Gui gui) {
-		this.gui = gui;
-	}
-
-	public void addEventHandlers() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException,
-	InvocationTargetException, InstantiationException {
-
-		// using reflection to avoid Mac specific classes being required for compiling KSE on other platforms
-		Class<?> applicationClass = Class.forName("com.apple.eawt.Application");
-		Class<?> quitHandlerClass;
-		Class<?> aboutHandlerClass;
-		Class<?> openFilesHandlerClass;
-		Class<?> preferencesHandlerClass;
-		
-		String version = System.getProperty("java.version");
-		String[] versionElements = version.split("\\.|_|-b");
-		
-		if (Double.parseDouble(versionElements[0]) >= 9) {
-			quitHandlerClass = Class.forName("java.awt.desktop.QuitHandler");
-			aboutHandlerClass = Class.forName("java.awt.desktop.AboutHandler");
-			openFilesHandlerClass = Class.forName("java.awt.desktop.OpenFilesHandler");
-			preferencesHandlerClass = Class.forName("java.awt.desktop.PreferencesHandler");
-		} else {
-			quitHandlerClass = Class.forName("com.apple.eawt.QuitHandler");
-			aboutHandlerClass = Class.forName("com.apple.eawt.AboutHandler");
-			openFilesHandlerClass = Class.forName("com.apple.eawt.OpenFilesHandler");
-			preferencesHandlerClass = Class.forName("com.apple.eawt.PreferencesHandler");    
-		}
-
-		Object application = applicationClass.getConstructor((Class[]) null).newInstance((Object[]) null);
-		Object proxy = Proxy.newProxyInstance(OSXHandlers.class.getClassLoader(), new Class<?>[]{
-			quitHandlerClass, aboutHandlerClass, openFilesHandlerClass, preferencesHandlerClass}, this);
-
-		applicationClass.getDeclaredMethod("setQuitHandler", quitHandlerClass).invoke(application, proxy);
-		applicationClass.getDeclaredMethod("setAboutHandler", aboutHandlerClass).invoke(application, proxy);
-		applicationClass.getDeclaredMethod("setOpenFileHandler", openFilesHandlerClass).invoke(application, proxy);
-		applicationClass.getDeclaredMethod("setPreferencesHandler", preferencesHandlerClass).invoke(application,
-				proxy);
-	}
-
-	@Override
-	public Object invoke(Object proxy, Method method, Object[] args) throws Throwable {
-		/*if ("openFiles".equals(method.getName())) {
-			if (args[0] != null) {
-				Object files = args[0].getClass().getMethod("getFiles").invoke(args[0]);
-				if (files instanceof List) {
-					OpenAction openAction = new OpenAction(kseFrame);
-					for (File file : (List<File>) files) {
-						openAction.openKeyStore(file);
-					}
-				}
-			}
-		} else */if ("handleQuitRequestWith".equals(method.getName())) {
-			gui.exit();
-			// If we have returned from the above call the user has decied not to quit
-			if (args[1] != null) {
-				args[1].getClass().getDeclaredMethod("cancelQuit").invoke(args[1]);
-			}
-		} else if ("handleAbout".equals(method.getName())) {
-			gui.about();
-		} else if ("handlePreferences".equals(method.getName())) {
-			PreferencesDialog.showPreferences(Gui.frame);
-			//EditPreferences editPreferences = new EditPreferences(frame, async);
-			//editPreferences.preferences();
-			gui.getFileTree().setExpandibleIcons(!IBioSimPreferences.INSTANCE.isPlusMinusIconsEnabled());
-			if (gui.getSBOLDocument() != null) {
-				gui.getSBOLDocument().setDefaultURIprefix(SBOLEditorPreferences.INSTANCE.getUserInfo().getURI().toString());
-			}
-		}
-		return null;
-	}
-
-}

learn/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>

log4j2.xml

@@ -1,65 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Configuration status="WARN" name="XMLConfigTest" packages="org.sbml.*">
-  <Properties>
-    <Property name="filename">jsbml.log</Property>
-  </Properties>
-  <ThresholdFilter level="trace"/>
- 
-  <Appenders>
-    <Console name="console">
-      <PatternLayout pattern="%5p (%F:%L) - %m%n"/>
-    </Console>
-    <File name="file" fileName="${filename}">
-      <PatternLayout>
-        <pattern>%d %p %C{1.} [%t] %m%n</pattern>
-      </PatternLayout>
-    </File>
-  </Appenders>
- 
-  <Loggers>
-    <Logger name="org.sbml" level="info" additivity="false">
-      <AppenderRef ref="console"/>
-      <AppenderRef ref="file"/>
-    </Logger>
-
-<!--
-    <Logger name="org.sbml.jsbml.xml.stax.SBMLWriter" level="debug" additivity="false">
-      <AppenderRef ref="console"/>
-      <AppenderRef ref="file"/>      
-    </Logger>
-    
-    <Logger name="org.sbml.jsbml.xml.stax.SBMLReader" level="debug" additivity="false">
-      <AppenderRef ref="console"/>
-      <AppenderRef ref="file"/>      
-    </Logger>
--->
-<!--    
-# org.sbml.jsbml.test.SimpleSBaseChangeListener - DEBUG : it will display all add, remove or change event (lot of output when reading an SBML file)
-# org.sbml.jsbml.xml.parsers.SBMLCoreParser - ERROR to DEBUG : anything related to problems when parsing the SBML core elements.
-# org.sbml.jsbml.xml.parsers.StringParser - ERROR to DEBUG : (lot of output) display all the event when reading XHTML
-# org.sbml.jsbml.xml.parsers.AnnotationParser - DEBUG : output when reading non RDF annotations.
-# org.sbml.jsbml.xml.parsers.XMLNodeWriter - DEBUG : output events when writing XMLNode, so HTML block
-# org.sbml.jsbml.xml.stax.SBMLReader - ERROR to DEBUG : (lot of output) display all the event when reading an SBML file
-# org.sbml.jsbml.xml.stax.SBMLWriter - ERROR to DEBUG : (lot of output) display all the event when writing an SBML file
-# org.sbml.jsbml.util.StringTools - WARN : warning when there is a problem with the conversion of a String into a number or boolean.
-# org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler - WARN to DEBUG : (lot of output) display all the event when writing mathML
-# org.sbml.jsbml.xml.parsers.MathMLStaxParser - ERROR to DEBUG : (lot of output) display all the event when reading a MathML block
-# org.sbml.jsbml.SBMLDocument - ERROR to DEBUG : will display problems related to the checkConsistency call
-# org.sbml.jsbml.validator.SBMLValidator - DEBUG : will print the xml result file from http://sbml.org/validator/ with few others checks when the parsing is done
-# org.sbml.jsbml.util.SubModel - DEBUG : will print the details of the submodel building
-# org.sbml.jsbml.ASTNode - ERROR to DEBUG
-# org.sbml.jsbml.xml.parsers.AbstractReaderWriter - DEBUG : events when reading or writing L3 packages block (if the parser extends this abstract class)
-# org.sbml.jsbml.xml.parsers.QualParser - DEBUG : events when reading/writing the qual package/extension.
-# org.sbml.jsbml.ext.comp.CompModelPlugin - DEBUG: register and unregister debug output for the comp package id namespace
-# org.sbml.jsbml.ext.comp.ArraysSBasePlugin - DEBUG: register and unregister debug output for the arrays package id namespace
-# org.sbml.jsbml.Model - DEBUG: register and unregister debug output for the core package id namespace
-# org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser - DEBUG: debug output when reading and writing RDF annotations
-
-    
---> 
-    <Root level="info">
-      <AppenderRef ref="file"/>
-    </Root>
-  </Loggers>
- 
-</Configuration>

pom.xml

@@ -72,10 +72,10 @@
 			<plugin>
 				<!-- settings for javac. -->
 				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.5.1</version>
+				<version>3.8.1</version>
 				<configuration>
-					<source>1.8</source>
-					<target>1.8</target>
+					<source>11</source>
+					<target>11</target>
 
 					<testExcludes>
 						<exclude>edu/utah/ece/async/ibiosim/conversion/gcm2sbml/*.java</exclude>

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>

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>

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>

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>

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>

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>

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>

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>

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>

prismtest/Circuit0x8E/results.txt

@@ -0,0 +1,2 @@
+0.0
+0.0010947156623888129

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) ]

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

prismtest/SimpleChem.props

@@ -0,0 +1,5 @@
+// File generated by SBML-to-PRISM converter
+// Original file: SimpleChem.xml
+// @GeneticLogicLab
+
+P=? [F<=100 (S2 > 8)]

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

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>

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>

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>

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#" />

prismtest/SimpleHierchyModel/topModel.props

@@ -0,0 +1,4 @@
+// File generated by SBML-to-PRISM converter
+// Original file: SimpleHierchyModel/topModel.xml
+// @GeneticLogicLab
+

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

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>

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>

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))]

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

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)) ]
+

prismtest/results.txt

@@ -0,0 +1,2 @@
+0.0
+0.9997151321743104

synthesis/pom.xml

@@ -124,7 +124,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>

verification/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>