krlhBlupine/iBioSim
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity Actions

Merge branch 'master' of https://github.com/MyersResearchGroup/iBioSim

Browse source
This commit is contained in:
Chris Myers 2024-11-26 20:28:24 -07:00
commit d4d40a9084
38 changed files with 15112 additions and 27 deletions
Download patch file Download diff file Expand all files Collapse all files

4
README.md
View file

@ -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):

2
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java
View file

@ -541,8 +541,6 @@ public class Run extends CoreObservable implements ActionListener {
this.notifyObservers(message);
message.setLog("Saving PRISM Property file:\n" + filename.replace(".xml", ".pctl"));
this.notifyObservers(message);
// TODO: LUKAS
// bioModel.convertSBML2PRISM(logFile, filename);
LPN.convertLPN2PRISM(logFile, lhpnFile, filename.replace(".xml", ".prism"), bioModel.getSBMLDocument());
Preferences biosimrc = Preferences.userRoot();
String prismCmd = biosimrc.get("biosim.general.prism", "");

64
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java
View file

@ -19,9 +19,11 @@ import java.io.IOException;
import java.net.URI;
import java.util.HashMap;
import java.util.HashSet;
import java.lang.reflect.Method;
import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLWriter;
@ -33,11 +35,13 @@ import org.sbolstandard.core2.TopLevel;
import org.virtualparts.VPRException;
import org.virtualparts.VPRTripleStoreException;
// import edu.utah.ece.async.ibiosim.analysis.properties.AnalysisProperties;
import edu.utah.ece.async.ibiosim.dataModels.biomodel.parser.BioModel;
import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
import edu.utah.ece.async.ibiosim.dataModels.sbol.SBOLUtility;
import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.SBOLException;
import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObservable;
import org.sbml.jsbml.ext.comp.CompModelPlugin;
import org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin;
@ -89,7 +93,7 @@ public class Converter {
System.err.println("\t-esf Export SBML hierarchical models in a single output file.");
System.err.println("\t-f continue after first error");
System.err.println("\t-i allow SBOL document to be incomplete");
System.err.println("\t-l <language> specifies language (SBOL1/SBOL2/GenBank/FASTA/SBML) for output (default=SBOL2). To output FASTA or GenBank, no SBOL default URI prefix is needed.");
System.err.println("\t-l <language> specifies language (SBOL1/SBOL2/GenBank/FASTA/SBML/PRISM) for output (default=SBOL2). To output FASTA or GenBank, no SBOL default URI prefix is needed.");
System.err.println("\t-mf The name of the file that will be produced to hold the result of the main SBOL file, if SBOL file diff was selected.");
System.err.println("\t-n allow non-compliant URIs");
System.err.println("\t-o <outputFile> specifies the full path of the output file produced from the converter");
@ -129,6 +133,7 @@ public class Converter {
boolean sbolV1out = false; //-l
boolean sbolV2out = false; //-l
boolean sbmlOut = false; //-l
boolean prismOut = false; //-l
boolean compliant = true; //-n
boolean noOutput = false; //-no
boolean typesInURI = false; //-t
@ -137,6 +142,7 @@ public class Converter {
boolean isValidation = false; //indicate if only validate SBOL files
boolean topEnvir = false; // determines if there is a topEnvironment model to be instantiated
boolean CelloModel = false; // determines if Cello-based modeling should be done
boolean PrismUnbound = true; // determines if the prism model should be bound or unbound
String compFileResult = ""; //-cf
String compareFile = ""; //-e
@ -188,6 +194,9 @@ public class Converter {
case "-t":
typesInURI = true;
break;
case "-bound":
PrismUnbound = false;
break;
case "-s":
if(index+1 >= args.length || args[index+1].equals("-"))
{
@ -225,6 +234,11 @@ public class Converter {
sbolV2out = true;
++index;
}
else if (args[index+1].equals("PRISM"))
{
prismOut = true;
++index;
}
else
{
usage();
@ -412,7 +426,51 @@ public class Converter {
boolean isDirectory = file.isDirectory();
if (!isDirectory)
{
if(inputIsSBML)
if(inputIsSBML && prismOut)
{
SBMLDocument inputSBMLDoc;
try
{
// Read in the SBML
inputSBMLDoc = SBMLutilities.readSBML(fullInputFileName, null, null);
// Create BioModel to allow flattening
File path = new File(fullInputFileName);
BioModel bioModel = new BioModel(path.getParent());
bioModel.load(fullInputFileName);
// Check if BioModel is hierarchical by checking the number of submodels
bioModel.createCompPlugin();
if(bioModel.getListOfSubmodels().isEmpty())
{
// Not hierarchical
SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
}else {
// hierarchical, therefore flatten model
if (bioModel.flattenModel(true) != null) {
SBMLDocument sbml = bioModel.flattenModel(true);
SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
}
}
}
catch (XMLStreamException e)
{
System.err.println("ERROR: Invalid XML file");
e.printStackTrace();
}
catch (IOException e)
{
System.err.println("ERROR: Unable to read or write prism file");
e.printStackTrace();
}
catch (BioSimException e) {
System.err.println("ERROR: Invalid SBML file");
}
}else if(inputIsSBML)
{
SBOLDocument outSBOLDoc = new SBOLDocument();
SBMLDocument inputSBMLDoc;
@ -552,7 +610,6 @@ public class Converter {
SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
}
}
if (topModelId != null) {
SBMLDocument topModel = SBMLutilities.readSBML(outputDir + File.separator + vpr_output+ ".xml", null, null);
topModel.getModel().setId(topModelId);
@ -571,7 +628,6 @@ public class Converter {
e.printStackTrace();
}
}
if (doVPR) {
if (topEnvir) {
SBMLDocument topEnvironment = SBMLutilities.readSBML(environment, null, null);

532
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2PRISM.java Normal file
View file

@ -0,0 +1,532 @@
/*******************************************************************************
*
* This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
* for the latest version of iBioSim.
*
* Copyright (C) 2017 University of Utah
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the Apache License. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
*
*******************************************************************************/
package edu.utah.ece.async.ibiosim.conversion;
import java.io.File;
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;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference;
import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
/**
* Perform conversion from SBML to PRISM.
*
* @author Lukas Buecherl
* @author Chris Myers
* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim
* Contributors </a>
* @version %I%
*/
public class SBML2PRISM {
/*
* Convert SBML to Prism. Input: SBMLDocument, File, bound. Output: void
*
* Function takes in a SBML document and writes the prism conversion of the file
* in the same directory. The function also translates the constraint into a
* properties file that is written in the same directory in a separate file. The
* original filename is used for the prism and property file. The SBMML file
* ends in .xml, the prism file in .sm, and the properties file in .props.
*
* To run the converter use the following command: java -jar
* 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
*/
public static void convertSBML2PRISM(SBMLDocument sbmlDoc, String filename, boolean unbound) throws IOException {
Model model = sbmlDoc.getModel();
File file = new File(filename.replace(".xml", ".sm"));
// Opening and writing preamble to the file
FileWriter out = new FileWriter(file);
out.write("// File generated by SBML-to-PRISM converter\n");
out.write("// Original file: " + filename + "\n");
out.write("// @GeneticLogicLab\n");
out.write("\n");
out.write("ctmc\n");
out.write("\n");
// Set bound limit if bound model is selected
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");
*/
}
// 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);
compartmentList.add(compartment);
}
// 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
// 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);
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 }
}
// 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);
String id = checkReservedKeywordPrism(species.getId());
int inAmount = (int) species.getInitialAmount();
out.write("\n");
out.write("// Species " + id + "\n");
if (unbound) {
out.write("module " + id + "\n");
out.write("\n");
out.write(" " + id + " : " + "int init " + inAmount + ";\n");
out.write("\n");
} else {
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");
*/
}
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 && 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(" [" + 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");
String math = checkReserveKeywordMath(
SBMLutilities.convertMath2PrismProperty(reaction.getKineticLaw().getMath()), model);
// System.err.println(math);
// System.err.println(localParameterList);
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);
}
// System.err.println(math);
// Get the math for the reaction rate
out.write(" [" + reactionId + "] " + math + " > 0 -> " + math + " : true;\n");
out.write("\n");
}
out.write("endmodule\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) + ": " + speciesId + "\n");
out.write("rewards " + "\"" + speciesId + "\" true : " + speciesId + "; endrewards\n");
}
out.close();
writePRISMProperty(filename, model);
}
/*
* 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.
*/
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);
// Property preamble
property_out.write("// File generated by SBML-to-PRISM converter\n");
property_out.write("// Original file: " + filename + "\n");
property_out.write("// @GeneticLogicLab\n");
property_out.write("\n");
for (int i = 0; i < model.getConstraintCount(); i++) {
// Get and write translation of constraint
property_out.write(checkReserveKeywordMath(
SBMLutilities.convertMath2PrismProperty(model.getConstraint(i).getMath()), model));
}
property_out.close();
}
/*
* Check for reserved keywords as species names Input: (String) NameOfSpecies
* Output: (String) _NameOfSpecies
*
* Function checks if the name of a species is also a reserved keyword in the
* prism language. If that is the case, the species name is replaced by the
* species name lead by an underscore.
*/
private static String checkReservedKeywordPrism(String speciesname) {
// List of reserved keywords in the prism language
List<String> keywords = Arrays.asList("A", "bool", "clock", "const", "ctmc", "C", "double", "dtmc", "E",
"endinit", "endinvariant", "endmodule", "endobservables", "endrewards", "endsystem", "false", "formula",
"filter", "func", "F", "global", "G", "init", "invariant", "I", "int", "label", "max", "mdp", "min",
"module", "X", "nondeterministic", "observable", "observables", "of", "Pmax", "Pmin", "P", "pomdp",
"popta", "probabilistic", "prob", "pta", "rate", "rewards", "Rmax", "Rmin", "R", "S", "stochastic",
"system", "true", "U", "W");
// Check if species name is in the list
if (keywords.contains(speciesname)) {
return "_" + speciesname;
} else {
return speciesname;
}
}
/*
* Check for reserved keywords as species names in math properties Input:
* (String) NameOfSpecies, model sbmlDoc.getModel(); Output: (String)
* _NameOfSpecies
*
* Function checks if the name of a species in a math function is also a
* reserved keyword in the prism language. If that is the case, the species name
* in the function is replaced by the species name lead by an underscore.
*/
private static String checkReserveKeywordMath(String math, Model model) {
// List of reserved keywords in the prism language
List<String> keywords = Arrays.asList("A", "bool", "clock", "const", "ctmc", "C", "double", "dtmc", "E",
"endinit", "endinvariant", "endmodule", "endobservables", "endrewards", "endsystem", "false", "formula",
"filter", "func", "F", "global", "G", "init", "invariant", "I", "int", "label", "max", "mdp", "min",
"module", "X", "nondeterministic", "observable", "observables", "of", "Pmax", "Pmin", "P", "pomdp",
"popta", "probabilistic", "prob", "pta", "rate", "rewards", "Rmax", "Rmin", "R", "S", "stochastic",
"system", "true", "U", "W");
// Declaration of new string list
ArrayList<String> speciesString = new ArrayList<String>();
// Iterating over species, if species name is a reserved keyword add it to list
// speciesString
for (int i = 0; i < model.getSpeciesCount(); i++) {
Species species = model.getSpecies(i);
if (keywords.contains(species.getId())) {
speciesString.add(species.getId());
}
}
// System.err.println(speciesString);
// Iterate over list and replace species name
for (int i = 0; i < keywords.size(); i++) {
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 " + 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));
}
}
return math;
}
}

2
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -6399,7 +6399,7 @@ public class BioModel extends CoreObservable{
}
}
private ArrayList<String> getListOfSubmodels() throws XMLStreamException, IOException, BioSimException {
public ArrayList<String> getListOfSubmodels() throws XMLStreamException, IOException, BioSimException { // Changed private to public (Lukas)
ArrayList<String> comps = new ArrayList<String>();
if (this.getGridEnabledFromFile(filename.replace(".gcm",".xml"))) {

3
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java
View file

@ -1969,7 +1969,8 @@ public class SBMLutilities extends CoreObservable
{
String leftStr = convertMath2PrismProperty(math.getLeftChild());
String rightStr = convertMath2PrismProperty(math.getRightChild());
return "(" + leftStr + " ^ " + rightStr + ")";
//return "(" + leftStr + " ^ " + rightStr + ")";
return "pow(" + leftStr + " , " + rightStr + ")";
}
else if (math.getType() == ASTNode.Type.RATIONAL)
{

380
prismtest/Circuit0x8E/AmtRpart_module.xml Normal file
View file

@ -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>

41
prismtest/Circuit0x8E/AraCsensor_module.xml Normal file
View file

@ -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>

464
prismtest/Circuit0x8E/BetIpart_module.xml Normal file
View file

@ -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>

508
prismtest/Circuit0x8E/HlyIIRpart_module.xml Normal file
View file

@ -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>

41
prismtest/Circuit0x8E/LacIsensor_module.xml Normal file
View file

@ -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>

464
prismtest/Circuit0x8E/PhlFpart_module.xml Normal file
View file

@ -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>

41
prismtest/Circuit0x8E/TetRsensor_module.xml Normal file
View file

@ -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>

464
prismtest/Circuit0x8E/YFPpart_module.xml Normal file
View file

@ -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>

18
prismtest/Circuit0x8E/manifest.xml Normal file
View file

@ -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>

2
prismtest/Circuit0x8E/results.txt Normal file
View file

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

5
prismtest/Circuit0x8E/topModel.props Normal file
View file

@ -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) ]

518
prismtest/Circuit0x8E/topModel.sm Normal file
View file

@ -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

1489
prismtest/Circuit0x8E/topModel.xml Normal file
View file

File diff suppressed because it is too large Load diff

2009
prismtest/Circuit0x8E_010to100.xml Normal file
View file

File diff suppressed because it is too large Load diff

2103
prismtest/Circuit0x8E_LHF_010to100.xml Normal file
View file

File diff suppressed because it is too large Load diff

1427
prismtest/Majority_10_10.xml Normal file
View file

File diff suppressed because it is too large Load diff

5
prismtest/SimpleChem.props Normal file
View file

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

65
prismtest/SimpleChem.sm Normal file
View file

@ -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

222
prismtest/SimpleChem.xml Normal file
View file

@ -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>

263
prismtest/SimpleHierchyModel/DSensor.xml Normal file
View file

@ -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>

10
prismtest/SimpleHierchyModel/manifest.xml Normal file
View file

@ -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>

2
prismtest/SimpleHierchyModel/metadata.rdf Normal file
View file

@ -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#" />

4
prismtest/SimpleHierchyModel/topModel.props Normal file
View file

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

97
prismtest/SimpleHierchyModel/topModel.sm Normal file
View file

@ -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

132
prismtest/SimpleHierchyModel/topModel.xml Normal file
View file

@ -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>

139
prismtest/SimplerChem.xml Normal file
View file

@ -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>

1770
prismtest/Speed_Independent_10_10.xml Normal file
View file

File diff suppressed because it is too large Load diff

5
prismtest/Toggle_10_10.props Normal file
View file

@ -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))]

320
prismtest/Toggle_10_10.sm Normal file
View file

@ -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

1478
prismtest/Toggle_10_10.xml Normal file
View file

File diff suppressed because it is too large Load diff

10
prismtest/pro.csl Normal file
View file

@ -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)) ]

2
prismtest/results.txt Normal file
View file

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