Merge pull request #627 from MyersResearchGroup/sbml-to-prism
Merge of SBML2PRISM converter
This commit is contained in:
cjmyers
GitHub
commit
d81e0d7532
37 changed files with 15110 additions and 25 deletions
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@ -541,8 +541,6 @@ public class Run extends CoreObservable implements ActionListener {
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this.notifyObservers(message);
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message.setLog("Saving PRISM Property file:\n" + filename.replace(".xml", ".pctl"));
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this.notifyObservers(message);
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// TODO: LUKAS
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// bioModel.convertSBML2PRISM(logFile, filename);
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LPN.convertLPN2PRISM(logFile, lhpnFile, filename.replace(".xml", ".prism"), bioModel.getSBMLDocument());
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Preferences biosimrc = Preferences.userRoot();
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String prismCmd = biosimrc.get("biosim.general.prism", "");
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@ -19,9 +19,11 @@ import java.io.IOException;
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import java.net.URI;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.lang.reflect.Method;
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import javax.xml.stream.XMLStreamException;
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import org.sbml.jsbml.Model;
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import org.sbml.jsbml.SBMLDocument;
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import org.sbml.jsbml.SBMLException;
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import org.sbml.jsbml.SBMLWriter;
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@ -33,11 +35,13 @@ import org.sbolstandard.core2.TopLevel;
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import org.virtualparts.VPRException;
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import org.virtualparts.VPRTripleStoreException;
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// import edu.utah.ece.async.ibiosim.analysis.properties.AnalysisProperties;
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import edu.utah.ece.async.ibiosim.dataModels.biomodel.parser.BioModel;
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import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
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import edu.utah.ece.async.ibiosim.dataModels.sbol.SBOLUtility;
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import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
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import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.SBOLException;
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import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObservable;
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import org.sbml.jsbml.ext.comp.CompModelPlugin;
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import org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin;
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@ -89,7 +93,7 @@ public class Converter {
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System.err.println("\t-esf Export SBML hierarchical models in a single output file.");
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System.err.println("\t-f continue after first error");
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System.err.println("\t-i allow SBOL document to be incomplete");
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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.");
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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.");
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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.");
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System.err.println("\t-n allow non-compliant URIs");
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System.err.println("\t-o <outputFile> specifies the full path of the output file produced from the converter");
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@ -107,7 +111,7 @@ public class Converter {
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System.err.println("\t-tmID Set the ID of the top SBML model");
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System.exit(1);
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}
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/**
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* The main method.
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@ -129,6 +133,7 @@ public class Converter {
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boolean sbolV1out = false; //-l
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boolean sbolV2out = false; //-l
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boolean sbmlOut = false; //-l
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boolean prismOut = false; //-l
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boolean compliant = true; //-n
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boolean noOutput = false; //-no
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boolean typesInURI = false; //-t
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@ -137,7 +142,8 @@ public class Converter {
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boolean isValidation = false; //indicate if only validate SBOL files
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boolean topEnvir = false; // determines if there is a topEnvironment model to be instantiated
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boolean CelloModel = false; // determines if Cello-based modeling should be done
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boolean PrismUnbound = true; // determines if the prism model should be bound or unbound
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String compFileResult = ""; //-cf
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String compareFile = ""; //-e
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String mainFileResult = ""; //-mf
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@ -151,7 +157,7 @@ public class Converter {
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String urlVPR = ""; //The specified synbiohub repository the user wants VPR model generator to connect to.
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String environment ="";
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String topModelId = null;
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HashSet<String> ref_sbolInputFilePath = new HashSet<String>(); //rsbol
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int index = 0;
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@ -188,6 +194,9 @@ public class Converter {
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case "-t":
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typesInURI = true;
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break;
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case "-bound":
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PrismUnbound = false;
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break;
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case "-s":
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if(index+1 >= args.length || args[index+1].equals("-"))
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{
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@ -225,6 +234,11 @@ public class Converter {
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sbolV2out = true;
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++index;
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}
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else if (args[index+1].equals("PRISM"))
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{
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prismOut = true;
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++index;
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}
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else
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{
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usage();
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@ -412,7 +426,51 @@ public class Converter {
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boolean isDirectory = file.isDirectory();
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if (!isDirectory)
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{
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if(inputIsSBML)
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if(inputIsSBML && prismOut)
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{
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SBMLDocument inputSBMLDoc;
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try
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{
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// Read in the SBML
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inputSBMLDoc = SBMLutilities.readSBML(fullInputFileName, null, null);
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// Create BioModel to allow flattening
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File path = new File(fullInputFileName);
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BioModel bioModel = new BioModel(path.getParent());
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bioModel.load(fullInputFileName);
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// Check if BioModel is hierarchical by checking the number of submodels
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bioModel.createCompPlugin();
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if(bioModel.getListOfSubmodels().isEmpty())
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{
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// Not hierarchical
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SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
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}else {
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// hierarchical, therefore flatten model
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if (bioModel.flattenModel(true) != null) {
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SBMLDocument sbml = bioModel.flattenModel(true);
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SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
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}
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}
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}
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catch (XMLStreamException e)
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{
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System.err.println("ERROR: Invalid XML file");
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e.printStackTrace();
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}
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catch (IOException e)
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{
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System.err.println("ERROR: Unable to read or write prism file");
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e.printStackTrace();
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}
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catch (BioSimException e) {
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System.err.println("ERROR: Invalid SBML file");
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}
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}else if(inputIsSBML)
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{
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SBOLDocument outSBOLDoc = new SBOLDocument();
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SBMLDocument inputSBMLDoc;
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@ -497,13 +555,13 @@ public class Converter {
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circuit_name = circuit_name.replace(".xml", "");
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circuit_name = circuit_name.replace(".sbol", "");
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String vpr_output = circuit_name + "_topModule";
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if(!topLevelURIStr.isEmpty())
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{
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if (doVPR) {
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TopLevel top = sbolDoc.getTopLevel(URI.create(topLevelURIStr));
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SBOLDocument newSbolDoc = sbolDoc.createRecursiveCopy(top);
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try {
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newSbolDoc = VPRModelGenerator.generateModel(urlVPR, newSbolDoc, vpr_output);
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//newSbolDoc.write("C:\\Users\\elros\\Desktop\\TestingConverter\\VPRoutput.xml");
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@ -516,18 +574,18 @@ public class Converter {
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e.printStackTrace();
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}
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//generateSBMLFromSBOL(newSbolDoc, outputDir);
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for (ModuleDefinition moduleDef : newSbolDoc.getRootModuleDefinitions())
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{
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HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, moduleDef, newSbolDoc, CelloModel);
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SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
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}
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}
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else {
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ModuleDefinition topModuleDef = sbolDoc.getModuleDefinition(URI.create(topLevelURIStr));
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HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc, CelloModel);
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SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
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ModuleDefinition topModuleDef = sbolDoc.getModuleDefinition(URI.create(topLevelURIStr));
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HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, topModuleDef, sbolDoc, CelloModel);
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SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
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}
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}
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else
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@ -545,20 +603,19 @@ public class Converter {
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e.printStackTrace();
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}
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}
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for (ModuleDefinition moduleDef : sbolDoc.getRootModuleDefinitions())
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{
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HashMap<String,BioModel> models = SBOL2SBML.generateModel(outputDir, moduleDef, sbolDoc, CelloModel);
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SBMLutilities.exportSBMLModels(models, outputDir, outputFileName, noOutput, sbmlOut, singleSBMLOutput);
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}
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}
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if (topModelId != null) {
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SBMLDocument topModel = SBMLutilities.readSBML(outputDir + File.separator + vpr_output+ ".xml", null, null);
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topModel.getModel().setId(topModelId);
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SBMLWriter writer = new SBMLWriter();
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try {
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//SBMLutilities.removeUnusedNamespaces(sbml);
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//SBMLutilities.removeUnusedNamespaces(sbml);
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writer.writeSBMLToFile(topModel, outputDir + File.separator + topModelId + ".xml");
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}
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catch (SBMLException e) {
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@ -571,26 +628,25 @@ public class Converter {
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e.printStackTrace();
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}
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}
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if (doVPR) {
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if (topEnvir) {
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SBMLDocument topEnvironment = SBMLutilities.readSBML(environment, null, null);
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CompSBMLDocumentPlugin docPlugin = (CompSBMLDocumentPlugin) topEnvironment.getPlugin("comp");
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ExternalModelDefinition exte = docPlugin.getExternalModelDefinition("TopModel");
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exte.setId(vpr_output);
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exte.setSource(vpr_output + ".xml");
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//exte.setId("topModule");
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//exte.setSource("topModule.xml");
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CompModelPlugin SBMLplugin = (CompModelPlugin) topEnvironment.getModel().getPlugin("comp");
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Submodel top = SBMLplugin.getSubmodel("C1");
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top.setModelRef(vpr_output);
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//top.setModelRef("topModule");
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SBMLWriter writing = new SBMLWriter();
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writing.writeSBMLToFile(topEnvironment, outputDir + File.separator + "Simulation_Environment.xml");
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}
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}
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@ -0,0 +1,532 @@
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/*******************************************************************************
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*
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* This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
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* for the latest version of iBioSim.
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*
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* Copyright (C) 2017 University of Utah
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*
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* This library is free software; you can redistribute it and/or modify it
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* under the terms of the Apache License. A copy of the license agreement is provided
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* in the file named "LICENSE.txt" included with this software distribution
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* and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
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*
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*******************************************************************************/
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package edu.utah.ece.async.ibiosim.conversion;
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import java.io.File;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.sbml.jsbml.Compartment;
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import org.sbml.jsbml.LocalParameter;
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import org.sbml.jsbml.Model;
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import org.sbml.jsbml.Parameter;
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import org.sbml.jsbml.Reaction;
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import org.sbml.jsbml.SBMLDocument;
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import org.sbml.jsbml.Species;
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import org.sbml.jsbml.SpeciesReference;
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import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
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/**
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* Perform conversion from SBML to PRISM.
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*
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* @author Lukas Buecherl
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* @author Chris Myers
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* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim
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* Contributors </a>
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* @version %I%
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*/
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public class SBML2PRISM {
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/*
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* Convert SBML to Prism. Input: SBMLDocument, File, bound. Output: void
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*
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* Function takes in a SBML document and writes the prism conversion of the file
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* in the same directory. The function also translates the constraint into a
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* properties file that is written in the same directory in a separate file. The
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* original filename is used for the prism and property file. The SBMML file
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* ends in .xml, the prism file in .sm, and the properties file in .props.
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*
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* To run the converter use the following command: java -jar
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* conversion/target/iBioSim-conversion-3.1.0-SNAPSHOT-jar-with-dependencies.jar
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* -l PRISM YOURSBMLFILE.xml
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*
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* The function also allows the translation into a bound model by simply adding
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* the flag -bound
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*/
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public static void convertSBML2PRISM(SBMLDocument sbmlDoc, String filename, boolean unbound) throws IOException {
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Model model = sbmlDoc.getModel();
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File file = new File(filename.replace(".xml", ".sm"));
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// Opening and writing preamble to the file
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FileWriter out = new FileWriter(file);
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out.write("// File generated by SBML-to-PRISM converter\n");
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out.write("// Original file: " + filename + "\n");
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out.write("// @GeneticLogicLab\n");
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out.write("\n");
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out.write("ctmc\n");
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out.write("\n");
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// Set bound limit if bound model is selected
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if (!unbound) {
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System.err.println("Under Development");
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/*
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* double maxAmount = 0.0; for (int i = 0; i < model.getSpeciesCount(); i++) {
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* Species species = model.getSpecies(i); if (species.getInitialAmount() >
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* maxAmount) { maxAmount = species.getInitialAmount(); } }
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* out.write(" const int MAX_AMOUNT = " + (int) maxAmount + ";\n");
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*/
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}
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// Declaration of new Compartment list
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ArrayList<Compartment> compartmentList = new ArrayList<Compartment>();
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// Iterating over Compartments
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for (int i = 0; i < model.getCompartmentCount(); i++) {
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Compartment compartment = model.getCompartment(i);
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compartmentList.add(compartment);
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}
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// System.err.println("Compartment List: " + compartmentList + "\n");
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// Identify compartments and their size
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if (!compartmentList.isEmpty()) {
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out.write("// Compartment size\n");
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}
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for (int i = 0; i < compartmentList.size(); i++) {
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String id = checkReservedKeywordPrism(compartmentList.get(i).getId());
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// System.err.println("Id: " + id);
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Double size = compartmentList.get(i).getSize();
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// System.err.println("Size: " + size);
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if (!Double.isNaN(size)) {
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out.write("const double " + id + " = " + size + ";\n");
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}
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}
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// Identify model parameters
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// Declaration of new parameter list
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ArrayList<Parameter> parameterList = new ArrayList<Parameter>();
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// Iterating over Compartments
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for (int i = 0; i < model.getParameterCount(); i++) {
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Parameter parameter = model.getParameter(i);
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parameterList.add(parameter);
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}
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// System.err.println("Parameter List: " + parameterList + "\n");
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if (!parameterList.isEmpty()) {
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out.write("\n");
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out.write("// Model parameters\n");
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}
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for (int i = 0; i < parameterList.size(); i++) {
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String id = checkReservedKeywordPrism(parameterList.get(i).getId());
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Double value = parameterList.get(i).getValue();
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String name = parameterList.get(i).getName();
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if (!Double.isNaN(value)) {
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out.write("const double " + id + " = " + value + "; // " + name + "\n"); // if not null name
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}
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}
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// Identify reactions
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// Declaration of new reaction list
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ArrayList<Reaction> reactionList = new ArrayList<Reaction>();
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// Iterating over reactions
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for (int i = 0; i < model.getReactionCount(); i++) {
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Reaction reaction = model.getReaction(i);
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reactionList.add(reaction);
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}
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// System.err.println("Reaction List: " + reactionList + "\n");
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// Identify local model parameters
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// Declaration of new local parameter list
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ArrayList<LocalParameter> localParameterList = new ArrayList<LocalParameter>();
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// Iterating over local parameters
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for (int i = 0; i < reactionList.size(); i++) {
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for (int j = 0; j < reactionList.get(i).getKineticLaw().getLocalParameterCount(); j++) {
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LocalParameter localparameter = reactionList.get(i).getKineticLaw().getLocalParameter(j);
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localParameterList.add(localparameter);
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}
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}
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// while (localParameterList.remove(null));
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// System.err.println("LocalParameterList: " + localParameterList + "\n");
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ArrayList<LocalParameter> UpdatedlocalParameterList = new ArrayList<LocalParameter>();
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for (int i = 0; i < reactionList.size(); i++) {
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for (int j = 0; j < reactionList.get(i).getKineticLaw().getLocalParameterCount(); j++) {
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LocalParameter localparameter = reactionList.get(i).getKineticLaw().getLocalParameter(j);
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// System.err.println("localparameter: " + localparameter);
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if (localparameter != null) {
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if (localParameterList.contains(localparameter)) {
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reactionList.get(i).getKineticLaw().getLocalParameter(j)
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.setId("local_" + localparameter.getId() + "_" + i);
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// 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;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
*******************************************************************************/
|
||||
package edu.utah.ece.async.ibiosim.dataModels.biomodel.parser;
|
||||
|
||||
import java.io.File;
|
||||
import java.io.File;
|
||||
import java.io.FileNotFoundException;
|
||||
import java.io.FileWriter;
|
||||
import java.io.IOException;
|
||||
|
|
@ -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"))) {
|
||||
|
|
|
|||
|
|
@ -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
380
prismtest/Circuit0x8E/AmtRpart_module.xml
Normal 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
41
prismtest/Circuit0x8E/AraCsensor_module.xml
Normal 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
464
prismtest/Circuit0x8E/BetIpart_module.xml
Normal 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
508
prismtest/Circuit0x8E/HlyIIRpart_module.xml
Normal 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
41
prismtest/Circuit0x8E/LacIsensor_module.xml
Normal 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
464
prismtest/Circuit0x8E/PhlFpart_module.xml
Normal 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
41
prismtest/Circuit0x8E/TetRsensor_module.xml
Normal 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
464
prismtest/Circuit0x8E/YFPpart_module.xml
Normal 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
18
prismtest/Circuit0x8E/manifest.xml
Normal 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
2
prismtest/Circuit0x8E/results.txt
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
0.0
|
||||
0.0010947156623888129
|
||||
5
prismtest/Circuit0x8E/topModel.props
Normal file
5
prismtest/Circuit0x8E/topModel.props
Normal 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
518
prismtest/Circuit0x8E/topModel.sm
Normal 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
1489
prismtest/Circuit0x8E/topModel.xml
Normal file
File diff suppressed because it is too large
Load diff
2009
prismtest/Circuit0x8E_010to100.xml
Normal file
2009
prismtest/Circuit0x8E_010to100.xml
Normal file
File diff suppressed because it is too large
Load diff
2103
prismtest/Circuit0x8E_LHF_010to100.xml
Normal file
2103
prismtest/Circuit0x8E_LHF_010to100.xml
Normal file
File diff suppressed because it is too large
Load diff
1427
prismtest/Majority_10_10.xml
Normal file
1427
prismtest/Majority_10_10.xml
Normal file
File diff suppressed because it is too large
Load diff
5
prismtest/SimpleChem.props
Normal file
5
prismtest/SimpleChem.props
Normal 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
65
prismtest/SimpleChem.sm
Normal 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
222
prismtest/SimpleChem.xml
Normal 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
263
prismtest/SimpleHierchyModel/DSensor.xml
Normal 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
10
prismtest/SimpleHierchyModel/manifest.xml
Normal 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
2
prismtest/SimpleHierchyModel/metadata.rdf
Normal 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
4
prismtest/SimpleHierchyModel/topModel.props
Normal 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
97
prismtest/SimpleHierchyModel/topModel.sm
Normal 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
132
prismtest/SimpleHierchyModel/topModel.xml
Normal 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
139
prismtest/SimplerChem.xml
Normal 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
1770
prismtest/Speed_Independent_10_10.xml
Normal file
File diff suppressed because it is too large
Load diff
5
prismtest/Toggle_10_10.props
Normal file
5
prismtest/Toggle_10_10.props
Normal 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
320
prismtest/Toggle_10_10.sm
Normal 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
1478
prismtest/Toggle_10_10.xml
Normal file
File diff suppressed because it is too large
Load diff
10
prismtest/pro.csl
Normal file
10
prismtest/pro.csl
Normal 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
2
prismtest/results.txt
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
0.0
|
||||
0.9997151321743104
|
||||
Loading…
Add table
Add a link
Reference in a new issue