diff --git a/analysis/log4j2.xml b/analysis/log4j2.xml new file mode 100644 index 000000000..3432bd0a4 --- /dev/null +++ b/analysis/log4j2.xml @@ -0,0 +1,65 @@ + + + + jsbml.log + + + + + + + + + + %d %p %C{1.} [%t] %m%n + + + + + + + + + + + + + + + + + + diff --git a/analysis/pom.xml b/analysis/pom.xml index 734e35044..e1cce5cb0 100644 --- a/analysis/pom.xml +++ b/analysis/pom.xml @@ -6,7 +6,7 @@ edu.utah.ece.async iBioSim - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT ../ jar @@ -73,13 +73,13 @@ edu.utah.ece.async iBioSim-dataModels - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT edu.utah.ece.async LEMA-verification - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT diff --git a/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java b/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java index 901269b12..3b4a41381 100644 --- a/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java +++ b/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java @@ -50,6 +50,7 @@ import edu.utah.ece.async.ibiosim.dataModels.util.Executables; import edu.utah.ece.async.ibiosim.dataModels.util.Message; import edu.utah.ece.async.ibiosim.dataModels.util.MutableString; import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException; +import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObservable; import edu.utah.ece.async.ibiosim.dataModels.util.observe.CoreObservable; import edu.utah.ece.async.lema.verification.lpn.Abstraction; import edu.utah.ece.async.lema.verification.lpn.LPN; @@ -474,7 +475,11 @@ public class Run extends CoreObservable implements ActionListener { this.notifyObservers(message); reb2sac = exec.exec(command, env, work); - updateReb2SacProgress(); + ReadStream s1 = new ReadStream("stdin", reb2sac.getInputStream ()); + ReadStream s2 = new ReadStream("stderr", reb2sac.getErrorStream ()); + s1.start (); + s2.start (); + //updateReb2SacProgress(); exitValue = reb2sac.waitFor(); } @@ -844,6 +849,71 @@ public class Run extends CoreObservable implements ActionListener { } } } + + public class ReadStream implements Runnable { + String name; + InputStream is; + Thread thread; + + public ReadStream(String name, InputStream is) { + this.name = name; + this.is = is; + } + public void start () { + thread = new Thread (this); + thread.start (); + } + public void run () { + try { + InputStreamReader isr = new InputStreamReader (is); + BufferedReader br = new BufferedReader (isr); + double runTime = properties.getSimulationProperties().getRun() * properties.getSimulationProperties().getTimeLimit(); + double time = 0; + double oldTime = 0; + int runNum = 0; + int prog = 0; + while (true) { + String line = br.readLine (); + if (line == null) break; + if (name.equals("stdin")) { + try { + if (line.contains("Time")) { + time = Double.parseDouble(line.substring(line.indexOf('=') + 1, line.length())); + if (oldTime > time) { + runNum++; + } + oldTime = time; + time += (runNum * properties.getSimulationProperties().getTimeLimit()); + double d = ((time * 100) / runTime); + String s = d + ""; + double decimal = Double.parseDouble(s.substring(s.indexOf('.'), s.length())); + if (decimal >= 0.5) { + prog = (int) (Math.ceil(d)); + } else { + prog = (int) (d); + } + } + } + catch (Exception e) { + e.printStackTrace(); + } + if (parent!=null) { + message.setInteger(prog); + parent.send(RequestType.REQUEST_PROGRESS, message); + } else{ + System.out.println(line); + } + } else { + System.out.println ("[" + name + "] " + line); + } + } + is.close (); + } catch (Exception ex) { + System.out.println ("Problem reading stream " + name + "... :" + ex); + ex.printStackTrace (); + } + } + } private void updateReb2SacProgress() throws IOException { String error = ""; diff --git a/conversion/pom.xml b/conversion/pom.xml index 2cfb53831..8be28c112 100644 --- a/conversion/pom.xml +++ b/conversion/pom.xml @@ -6,7 +6,7 @@ edu.utah.ece.async iBioSim - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT ../ jar @@ -65,7 +65,7 @@ edu.utah.ece.async iBioSim-dataModels - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT diff --git a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2SBOL.java b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2SBOL.java index 1960d5f74..546f98671 100644 --- a/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2SBOL.java +++ b/conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2SBOL.java @@ -56,6 +56,7 @@ import org.sbolstandard.core2.SBOLValidationException; import org.sbolstandard.core2.Sequence; import org.sbolstandard.core2.SequenceOntology; import org.sbolstandard.core2.SystemsBiologyOntology; +import org.sbolstandard.core2.TopLevel; import edu.utah.ece.async.ibiosim.dataModels.biomodel.annotation.AnnotationUtility; import edu.utah.ece.async.ibiosim.dataModels.biomodel.parser.BioModel; @@ -140,6 +141,22 @@ public class SBML2SBOL { return parseSBMLModel("file:" + fileName, externalSBMLPath, sbmlDoc, sbmlDoc.getModel(), sbolDoc, sbol_Library); } + /** + * Remove SBOL objects by their displayId to avoid objects with same displayId but different + * URI prefix + * + * @param sbolDoc SBOL document to remove objects from + * @param displayId Display id to use to search for objects to remove + * @throws SBOLValidationException Thrown when there is a problem caused by removing the object + */ + public static void removeByDisplayId(SBOLDocument sbolDoc,String displayId) throws SBOLValidationException { + for (TopLevel topLevel : sbolDoc.getTopLevels()) { + if (topLevel.getDisplayId().contentEquals(displayId)) { + sbolDoc.removeTopLevel(topLevel); + } + } + } + /** * Convert the specified SBML model to its equivalent SBOL ModuleDefinition. * All SBML SBase referencing this SBML model will be converted to SBOL data object. @@ -175,6 +192,7 @@ public class SBML2SBOL { sbolDoc.removeModel(sbolModel); } + removeByDisplayId(sbolDoc,model.getId() + "_model"); sbolModel = sbolDoc.createModel(model.getId() + "_model", VERSION, sourceURI, LANGUAGE, FRAMEWORK); String identityStr = model.getId() + "_md"; @@ -182,6 +200,7 @@ public class SBML2SBOL { if (moduleDef!=null) { sbolDoc.removeModuleDefinition(moduleDef); } + removeByDisplayId(sbolDoc,identityStr); moduleDef = sbolDoc.createModuleDefinition(identityStr, VERSION); moduleDef.addModel(sbolModel); @@ -378,11 +397,13 @@ public class SBML2SBOL { } compDef = sbolDoc.getComponentDefinition(compDef_identity, VERSION); if (compDef==null) { + removeByDisplayId(sbolDoc,compDef_identity); compDef = sbolDoc.createComponentDefinition(compDef_identity, VERSION, compDef_type); compDef.setName(species.getId()); compDef.setRoles(compDef_role); } else if (!compDef.getTypes().containsAll(compDef_type)) { sbolDoc.removeComponentDefinition(compDef); + removeByDisplayId(sbolDoc,compDef_identity); compDef = sbolDoc.createComponentDefinition(compDef_identity, VERSION, compDef_type); compDef.setName(species.getId()); compDef.setRoles(compDef_role); diff --git a/dataModels/log4j2.xml b/dataModels/log4j2.xml new file mode 100644 index 000000000..3432bd0a4 --- /dev/null +++ b/dataModels/log4j2.xml @@ -0,0 +1,65 @@ + + + + jsbml.log + + + + + + + + + + %d %p %C{1.} [%t] %m%n + + + + + + + + + + + + + + + + + + diff --git a/dataModels/pom.xml b/dataModels/pom.xml index 7ecc984b9..d78e7bbe9 100644 --- a/dataModels/pom.xml +++ b/dataModels/pom.xml @@ -6,7 +6,7 @@ edu.utah.ece.async iBioSim - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT ../ jar @@ -71,7 +71,7 @@ org.sbml.jsbml jsbml - 1.4 + 1.6-SNAPSHOT @@ -132,7 +132,7 @@ edu.utah.ece.async iBioSim-libsbml - 5.16.0-SNAPSHOT + 5.18.0-SNAPSHOT diff --git a/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java b/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java index b19e4a258..358eab71a 100644 --- a/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java +++ b/dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/util/SBMLutilities.java @@ -76,10 +76,6 @@ import org.sbml.jsbml.ext.comp.ReplacedBy; import org.sbml.jsbml.ext.comp.ReplacedElement; import org.sbml.jsbml.ext.comp.SBaseRef; import org.sbml.jsbml.ext.comp.Submodel; -import org.sbml.jsbml.ext.distrib.DistribConstants; -import org.sbml.jsbml.ext.distrib.DistribFunctionDefinitionPlugin; -import org.sbml.jsbml.ext.distrib.DistribInput; -import org.sbml.jsbml.ext.distrib.DrawFromDistribution; import org.sbml.jsbml.ext.fbc.FBCConstants; import org.sbml.jsbml.ext.fbc.FBCModelPlugin; import org.sbml.jsbml.ext.fbc.FBCReactionPlugin; @@ -90,10 +86,7 @@ import org.sbml.jsbml.ext.layout.LayoutModelPlugin; import org.sbml.jsbml.text.parser.FormulaParserLL3; import org.sbml.jsbml.text.parser.IFormulaParser; import org.sbml.jsbml.text.parser.ParseException; -import org.sbml.jsbml.xml.XMLAttributes; -import org.sbml.jsbml.xml.XMLNamespaces; import org.sbml.jsbml.xml.XMLNode; -import org.sbml.jsbml.xml.XMLTriple; import org.sbml.libsbml.ConversionProperties; import org.sbml.libsbml.SBMLNamespaces; import org.sbml.libsbml.SBasePlugin; @@ -3138,35 +3131,35 @@ public class SBMLutilities extends CoreObservable createFunction(model, "bernoulli", "Bernoulli distribution", "lambda(p,p)"); } - public static void createDistribution(FunctionDefinition f, String[] inputTypes, String[] inputs, String distribution) - { - DistribFunctionDefinitionPlugin distrib = SBMLutilities.getDistribFunctionDefinitionPlugin(f); - DrawFromDistribution draw = distrib.createDrawFromDistribution(); - for (int i = 0; i < inputs.length; i++) - { - DistribInput input = draw.createDistribInput(); - input.setId(inputs[i]); - input.setIndex(i); - } - // UncertML element - XMLNode xmlNode = new XMLNode(new XMLTriple("UncertML"), new XMLAttributes(), new XMLNamespaces()); - xmlNode.addNamespace("http://www.uncertml.org/3.0"); - - // NormalDistribution element - XMLNode distNode = new XMLNode(new XMLTriple(distribution), new XMLAttributes(), new XMLNamespaces()); - distNode.addAttr("definition", "http://www.uncertml.org/distributions"); - xmlNode.addChild(distNode); - - for (int i = 0; i < inputs.length; i++) - { - XMLNode inputNode = new XMLNode(new XMLTriple(inputTypes[i]), new XMLAttributes(), new XMLNamespaces()); - distNode.addChild(inputNode); - XMLNode varNode = new XMLNode(new XMLTriple("var"), new XMLAttributes(), new XMLNamespaces()); - varNode.addAttr("varId", inputs[i]); - inputNode.addChild(varNode); - } -// draw.setUncertML(xmlNode); - } +// public static void createDistribution(FunctionDefinition f, String[] inputTypes, String[] inputs, String distribution) +// { +// DistribFunctionDefinitionPlugin distrib = SBMLutilities.getDistribFunctionDefinitionPlugin(f); +// DrawFromDistribution draw = distrib.createDrawFromDistribution(); +// for (int i = 0; i < inputs.length; i++) +// { +// DistribInput input = draw.createDistribInput(); +// input.setId(inputs[i]); +// input.setIndex(i); +// } +// // UncertML element +// XMLNode xmlNode = new XMLNode(new XMLTriple("UncertML"), new XMLAttributes(), new XMLNamespaces()); +// xmlNode.addNamespace("http://www.uncertml.org/3.0"); +// +// // NormalDistribution element +// XMLNode distNode = new XMLNode(new XMLTriple(distribution), new XMLAttributes(), new XMLNamespaces()); +// distNode.addAttr("definition", "http://www.uncertml.org/distributions"); +// xmlNode.addChild(distNode); +// +// for (int i = 0; i < inputs.length; i++) +// { +// XMLNode inputNode = new XMLNode(new XMLTriple(inputTypes[i]), new XMLAttributes(), new XMLNamespaces()); +// distNode.addChild(inputNode); +// XMLNode varNode = new XMLNode(new XMLTriple("var"), new XMLAttributes(), new XMLNamespaces()); +// varNode.addAttr("varId", inputs[i]); +// inputNode.addChild(varNode); +// } +//// draw.setUncertML(xmlNode); +// } /** * Add a new function @@ -3194,50 +3187,50 @@ public class SBMLutilities extends CoreObservable if (id.equals("uniform")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Uniform_distribution_(continuous)"); - SBMLutilities.createDistribution(f, new String[] { "minimum", "maximum" }, new String[] { "a", "b" }, "UniformDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "minimum", "maximum" }, new String[] { "a", "b" }, "UniformDistribution"); } else if (id.equals("normal")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Normal_distribution"); - SBMLutilities.createDistribution(f, new String[] { "mean", "stddev" }, new String[] { "m", "s" }, "NormalDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "mean", "stddev" }, new String[] { "m", "s" }, "NormalDistribution"); } else if (id.equals("exponential")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Exponential_distribution"); - SBMLutilities.createDistribution(f, new String[] { "rate" }, new String[] { "l" }, "ExponentialDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "rate" }, new String[] { "l" }, "ExponentialDistribution"); } else if (id.equals("gamma")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Gamma_distribution"); - SBMLutilities.createDistribution(f, new String[] { "shape", "scale" }, new String[] { "a", "b" }, "GammaDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "shape", "scale" }, new String[] { "a", "b" }, "GammaDistribution"); } else if (id.equals("poisson")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Poisson_distribution"); - SBMLutilities.createDistribution(f, new String[] { "rate" }, new String[] { "mu" }, "PoissonDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "rate" }, new String[] { "mu" }, "PoissonDistribution"); } else if (id.equals("lognormal")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Log-normal_distribution"); // TODO: check order - SBMLutilities.createDistribution(f, new String[] { "shape", "logScale" }, new String[] { "sh", "lsc" }, "GammaDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "shape", "logScale" }, new String[] { "sh", "lsc" }, "GammaDistribution"); } else if (id.equals("chisq")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Chi-squared_distribution"); - SBMLutilities.createDistribution(f, new String[] { "degreeOfFreedom" }, new String[] { "nu" }, "ChiSquareDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "degreeOfFreedom" }, new String[] { "nu" }, "ChiSquareDistribution"); } else if (id.equals("laplace")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Laplace_distribution"); // TODO: mine only has one param? - SBMLutilities.createDistribution(f, new String[] { "location", "scale" }, new String[] { "l", "s" }, "LaplaceDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "location", "scale" }, new String[] { "l", "s" }, "LaplaceDistribution"); } else if (id.equals("cauchy")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Cauchy_distribution"); // TODO: mine only has one param? - SBMLutilities.createDistribution(f, new String[] { "location", "scale" }, new String[] { "l", "s" }, "CauchyDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "location", "scale" }, new String[] { "l", "s" }, "CauchyDistribution"); } else if (id.equals("rayleigh")) { @@ -3247,13 +3240,13 @@ public class SBMLutilities extends CoreObservable else if (id.equals("binomial")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Binomial_distribution"); - SBMLutilities.createDistribution(f, new String[] { "probabilityOfSuccess", "numberOfTrials" }, new String[] { "p", "n" }, - "BinomialDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "probabilityOfSuccess", "numberOfTrials" }, new String[] { "p", "n" }, + // "BinomialDistribution"); } else if (id.equals("bernoulli")) { AnnotationUtility.setDistributionAnnotation(f, "http://en.wikipedia.org/wiki/Bernoulli_distribution"); - SBMLutilities.createDistribution(f, new String[] { "categoryProb" }, new String[] { "p" }, "BernoulliDistribution"); + //SBMLutilities.createDistribution(f, new String[] { "categoryProb" }, new String[] { "p" }, "BernoulliDistribution"); } } } @@ -4937,16 +4930,16 @@ public class SBMLutilities extends CoreObservable return null; } - public static DistribFunctionDefinitionPlugin getDistribFunctionDefinitionPlugin(FunctionDefinition function) - { - if (function.getExtension(DistribConstants.namespaceURI) != null) - { - return (DistribFunctionDefinitionPlugin) function.getExtension(DistribConstants.namespaceURI); - } - DistribFunctionDefinitionPlugin distrib = new DistribFunctionDefinitionPlugin(function); - function.addExtension(DistribConstants.namespaceURI, distrib); - return distrib; - } +// public static DistribFunctionDefinitionPlugin getDistribFunctionDefinitionPlugin(FunctionDefinition function) +// { +// if (function.getExtension(DistribConstants.namespaceURI) != null) +// { +// return (DistribFunctionDefinitionPlugin) function.getExtension(DistribConstants.namespaceURI); +// } +// DistribFunctionDefinitionPlugin distrib = new DistribFunctionDefinitionPlugin(function); +// function.addExtension(DistribConstants.namespaceURI, distrib); +// return distrib; +// } public static LayoutModelPlugin getLayoutModelPlugin(Model model) { diff --git a/gui/pom.xml b/gui/pom.xml index b3ce5c7db..e720df673 100644 --- a/gui/pom.xml +++ b/gui/pom.xml @@ -6,7 +6,7 @@ edu.utah.ece.async iBioSim - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT ../ jar @@ -123,38 +123,38 @@ edu.utah.ece.async iBioSim-dataModels - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT edu.utah.ece.async iBioSim-conversion - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT edu.utah.ece.async iBioSim-learn - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT edu.utah.ece.async iBioSim-analysis - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT edu.utah.ece.async iBioSim-synthesis - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT edu.utah.ece.async.sboldesigner SBOLDesigner - 3.1-SNAPSHOT + 3.1 diff --git a/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java b/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java index 728387490..9cfb9275e 100644 --- a/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java +++ b/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java @@ -4138,12 +4138,15 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot public void createIBioSimActivity() throws Exception { Activity iBioSimActivity = sbolDocument.getActivity(currentProjectId + "_iBioSim_activity", "1"); - if (iBioSimActivity==null) { + if (iBioSimActivity==null) { + SBML2SBOL.removeByDisplayId(sbolDocument,currentProjectId + "_iBioSim_activity"); iBioSimActivity = sbolDocument.createActivity(currentProjectId + "_iBioSim_activity", "1"); Association association = iBioSimActivity.createAssociation("association", URI.create("https://synbiohub.org/public/SBOL_Software/iBioSim/"+iBioSimVersion)); + SBML2SBOL.removeByDisplayId(sbolDocument,currentProjectId + "_plan"); Plan plan = sbolDocument.createPlan(currentProjectId + "_plan", "1"); association.setPlan(plan.getIdentity()); + SBML2SBOL.removeByDisplayId(sbolDocument,currentProjectId + "_sedml"); Attachment sedmlFile = sbolDocument.createAttachment(currentProjectId + "_sedml", "1", URI.create("file:" + currentProjectId + ".sedml")); sedmlFile.setName(currentProjectId + ".sedml"); @@ -4174,6 +4177,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot root + File.separator + output.getId()+".png",GraphData.PNG_FILE_TYPE,650,400); Attachment pngFile = sbolDocument.getAttachment(output.getId()+"_png","1"); if (pngFile==null) { + SBML2SBOL.removeByDisplayId(sbolDocument,output.getId()+"_png"); pngFile = sbolDocument.createAttachment(output.getId()+"_png", "1", URI.create("file:"+output.getId()+".png")); pngFile.setFormat(URI.create("http://identifiers.org/edam/format_3603")); @@ -4189,6 +4193,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot root + File.separator + output.getId()+".png",GraphData.PNG_FILE_TYPE,650,400); Attachment pngFile = sbolDocument.getAttachment(output.getId()+"_png","1"); if (pngFile==null) { + SBML2SBOL.removeByDisplayId(sbolDocument,output.getId()+"_png"); pngFile = sbolDocument.createAttachment(output.getId()+"_png", "1", URI.create("file:"+output.getId()+".png")); pngFile.setFormat(URI.create("http://identifiers.org/edam/format_3603")); diff --git a/learn/pom.xml b/learn/pom.xml index d9c0d0f65..75e68f4e5 100644 --- a/learn/pom.xml +++ b/learn/pom.xml @@ -5,7 +5,7 @@ iBioSim-learn edu.utah.ece.async - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT ../ iBioSim @@ -65,7 +65,7 @@ edu.utah.ece.async iBioSim-analysis - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT diff --git a/lib/libsbmlj.jar b/lib/libsbmlj.jar index 7fdca2062..d2f4ff25a 100755 Binary files a/lib/libsbmlj.jar and b/lib/libsbmlj.jar differ diff --git a/log4j2.xml b/log4j2.xml new file mode 100644 index 000000000..3432bd0a4 --- /dev/null +++ b/log4j2.xml @@ -0,0 +1,65 @@ + + + + jsbml.log + + + + + + + + + + %d %p %C{1.} [%t] %m%n + + + + + + + + + + + + + + + + + + diff --git a/pom.xml b/pom.xml index cd6593ede..26c6a02ae 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ 4.0.0 edu.utah.ece.async iBioSim - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT pom iBioSim CAD tool aimed for the modeling, analysis, and design of genetic circuits. This tool supports both SBML and SBOL data models. diff --git a/synthesis/pom.xml b/synthesis/pom.xml index a27bcc0fb..4bcfa68c7 100644 --- a/synthesis/pom.xml +++ b/synthesis/pom.xml @@ -6,7 +6,7 @@ edu.utah.ece.async iBioSim - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT ../ jar @@ -35,12 +35,12 @@ edu.utah.ece.async LEMA-verification - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT edu.utah.ece.async iBioSim-dataModels - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT org.sbml.jsbml @@ -60,7 +60,7 @@ edu.utah.ece.async iBioSim-conversion - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT diff --git a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/nandTm1.xml b/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/nandTm1.xml deleted file mode 100644 index 8c7bb0631..000000000 --- a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/nandTm1.xml +++ /dev/null @@ -1,3696 +0,0 @@ - - - - - tu_pAmeRpAmtRE1_BetI_module - 1 - - - - E1_BetI_fc - 1 - - - - - - - BetI_mapsTo - 1 - - - - - - - - - - - pAmtR - 1 - - - - - - - - - BetI_protein - 1 - - - - - - - - - tu_pAmeRpAmtRE1_BetI_fc - 1 - - - - - - - pAmtR_mapsTo - 1 - - - - - - - - - E1_BetI_mapsTo - 1 - - - - - - - - - pAmeR_mapsTo - 1 - - - - - - - - - - - AmeR_protein - 1 - - - - - - - - - BetI - 1 - - - - - - - - - AmtR_protein - 1 - - - - - - - - - pAmeR - 1 - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_BetI_protein_production_sub - 1 - - - - - tu_pAmeRpAmtRE1_BetI_module_BetI_protein_production_sub_BetI_BetI - 1 - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_BetI_protein_production_sub_BetI_protein_BetI_protein - 1 - - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_BetI_protein_degradation_sub - 1 - - - - - tu_pAmeRpAmtRE1_BetI_module_BetI_protein_degradation_sub_BetI_protein_BetI_protein - 1 - - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_AmtR_protein_degradation_sub - 1 - - - - - tu_pAmeRpAmtRE1_BetI_module_AmtR_protein_degradation_sub_AmtR_protein_AmtR_protein - 1 - - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_AmtR_pAmtR_repression_sub - 1 - - - - - tu_pAmeRpAmtRE1_BetI_module_AmtR_pAmtR_repression_sub_AmtR_protein_AmtR_protein - 1 - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_AmtR_pAmtR_repression_sub_pAmtR_pAmtR - 1 - - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_AmeR_pAmeR_repression_sub - 1 - - - - - tu_pAmeRpAmtRE1_BetI_module_AmeR_pAmeR_repression_sub_AmeR_protein_AmeR_protein - 1 - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_AmeR_pAmeR_repression_sub_pAmeR_pAmeR - 1 - - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_module_AmeR_protein_degradation_sub - 1 - - - - - tu_pAmeRpAmtRE1_BetI_module_AmeR_protein_degradation_sub_AmeR_protein_AmeR_protein - 1 - - - - - - - - - - - AmeR_pAmeR_repression - 1 - - - - pAmeR - 1 - - - - - - - - - AmeR_protein - 1 - - - - - - - - - AmeR_pAmeR_repression - 1 - - - - - AmeR_protein_participation - 1 - - - - - - - - pAmeR_promoter_participation - 1 - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module - 1 - - - - pIcaRA - 1 - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_fc - 1 - - - - - - - pBetI_mapsTo - 1 - - - - - - - - - A1_AmtR_mapsTo - 1 - - - - - - - - - pIcaRA_mapsTo - 1 - - - - - - - - - - - BetI_protein - 1 - - - - - - - - - AmtR_protein - 1 - - - - - - - - - AmtR - 1 - - - - - - - - - pBetI - 1 - - - - - - - - - A1_AmtR_fc - 1 - - - - - - - AmtR_mapsTo - 1 - - - - - - - - - - - IcaRA_protein - 1 - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_BetI_protein_degradation_sub - 1 - - - - - tu_pBetIpIcaRAA1_AmtR_module_BetI_protein_degradation_sub_BetI_protein_BetI_protein - 1 - - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_IcaRA_pIcaRA_repression_sub - 1 - - - - - tu_pBetIpIcaRAA1_AmtR_module_IcaRA_pIcaRA_repression_sub_pIcaRA_pIcaRA - 1 - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_IcaRA_pIcaRA_repression_sub_IcaRA_protein_IcaRA_protein - 1 - - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_BetI_pBetI_repression_sub - 1 - - - - - tu_pBetIpIcaRAA1_AmtR_module_BetI_pBetI_repression_sub_pBetI_pBetI - 1 - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_BetI_pBetI_repression_sub_BetI_protein_BetI_protein - 1 - - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_AmtR_protein_degradation_sub - 1 - - - - - tu_pBetIpIcaRAA1_AmtR_module_AmtR_protein_degradation_sub_AmtR_protein_AmtR_protein - 1 - - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_AmtR_protein_production_sub - 1 - - - - - tu_pBetIpIcaRAA1_AmtR_module_AmtR_protein_production_sub_AmtR_protein_AmtR_protein - 1 - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_AmtR_protein_production_sub_AmtR_AmtR - 1 - - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_module_IcaRA_protein_degradation_sub - 1 - - - - - tu_pBetIpIcaRAA1_AmtR_module_IcaRA_protein_degradation_sub_IcaRA_protein_IcaRA_protein - 1 - - - - - - - - - - - AmeR_protein_production - 1 - - - - AmeR_protein - 1 - - - - - - - - - AmeR - 1 - - - - - - - - - AmeR_protein_interaction - 1 - - - - - AmeR - 1 - - - - - - - - AmeR_protein - 1 - - - - - - - - - - HlyIIR_protein_degradation - 1 - - - - HlyIIR_protein - 1 - - - - - - - - - HlyIIR_degradation_interaction - 1 - - - - - HlyIIR_protein - 1 - - - - - - - - - - IcaRA_protein_production - 1 - - - - IcaRA_protein - 1 - - - - - - - - - IcaRA - 1 - - - - - - - - - IcaRA_protein_interaction - 1 - - - - - IcaRA - 1 - - - - - - - - IcaRA_protein - 1 - - - - - - - - - - tu_pBM3R1F1_AmeR_module - 1 - - - - AmeR_protein - 1 - - - - - - - - - pBM3R1 - 1 - - - - - - - - - tu_pBM3R1F1_AmeR_fc - 1 - - - - - - - pBM3R1_mapsTo - 1 - - - - - - - - - F1_AmeR_mapsTo - 1 - - - - - - - - - - - BM3R1_protein - 1 - - - - - - - - - AmeR - 1 - - - - - - - - - F1_AmeR_fc - 1 - - - - - - - AmeR_mapsTo - 1 - - - - - - - - - - - tu_pBM3R1F1_AmeR_module_AmeR_protein_production_sub - 1 - - - - - tu_pBM3R1F1_AmeR_module_AmeR_protein_production_sub_AmeR_AmeR - 1 - - - - - - - - - tu_pBM3R1F1_AmeR_module_AmeR_protein_production_sub_AmeR_protein_AmeR_protein - 1 - - - - - - - - - - - tu_pBM3R1F1_AmeR_module_AmeR_protein_degradation_sub - 1 - - - - - tu_pBM3R1F1_AmeR_module_AmeR_protein_degradation_sub_AmeR_protein_AmeR_protein - 1 - - - - - - - - - - - tu_pBM3R1F1_AmeR_module_BM3R1_pBM3R1_repression_sub - 1 - - - - - tu_pBM3R1F1_AmeR_module_BM3R1_pBM3R1_repression_sub_pBM3R1_pBM3R1 - 1 - - - - - - - - - tu_pBM3R1F1_AmeR_module_BM3R1_pBM3R1_repression_sub_BM3R1_protein_BM3R1_protein - 1 - - - - - - - - - - - tu_pBM3R1F1_AmeR_module_BM3R1_protein_degradation_sub - 1 - - - - - tu_pBM3R1F1_AmeR_module_BM3R1_protein_degradation_sub_BM3R1_protein_BM3R1_protein - 1 - - - - - - - - - - - BetI_protein_degradation - 1 - - - - BetI_protein - 1 - - - - - - - - - BetI_degradation_interaction - 1 - - - - - BetI_protein - 1 - - - - - - - - - - BM3R1_pBM3R1_repression - 1 - - - - BM3R1_protein - 1 - - - - - - - - - pBM3R1 - 1 - - - - - - - - - BM3R1_pBM3R1_repression - 1 - - - - - pBM3R1_promoter_participation - 1 - - - - - - - - BM3R1_protein_participation - 1 - - - - - - - - - - BetI_pBetI_repression - 1 - - - - BetI_protein - 1 - - - - - - - - - pBetI - 1 - - - - - - - - - BetI_pBetI_repression - 1 - - - - - pBetI_promoter_participation - 1 - - - - - - - - BetI_protein_participation - 1 - - - - - - - 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1 - - - - - AmeR_protein - 1 - - - - - - - - - - IcaRA_protein_degradation - 1 - - - - IcaRA_protein - 1 - - - - - - - - - IcaRA_degradation_interaction - 1 - - - - - IcaRA_protein - 1 - - - - - - - - - - AmtR_protein_degradation - 1 - - - - AmtR_protein - 1 - - - - - - - - - AmtR_degradation_interaction - 1 - - - - - AmtR_protein - 1 - - - - - - - - - - AmtR_pAmtR_repression - 1 - - - - AmtR_protein - 1 - - - - - - - - - pAmtR - 1 - - - - - - - - - AmtR_pAmtR_repression - 1 - - - - - AmtR_protein_participation - 1 - - - - - - - - pAmtR_promoter_participation - 1 - - - - - - - - - - BM3R1_protein_degradation - 1 - - - - BM3R1_protein - 1 - - - - - - - - - BM3R1_degradation_interaction - 1 - - - - - BM3R1_protein - 1 - - - - - - - - - - BetI_protein_production - 1 - - - - BetI - 1 - - - - - - - - - BetI_protein - 1 - - - - - - - - - BetI_protein_interaction - 1 - - - - - BetI - 1 - - - - - - - - BetI_protein - 1 - - - - - - - - - - AmtR_protein_production - 1 - - - - AmtR_protein - 1 - - - - - - - - - AmtR - 1 - - - - - - - - - AmtR_protein_interaction - 1 - - - - - AmtR - 1 - - - - - - - - AmtR_protein - 1 - - - - - - - - - - IcaRA_pIcaRA_repression - 1 - - - - pIcaRA - 1 - - - - - - - - - IcaRA_protein - 1 - - - - - - - - - IcaRA_pIcaRA_repression - 1 - - - - - pIcaRA_promoter_participation - 1 - - - - - - - - IcaRA_protein_participation - 1 - - - - - - - - - - tu_pHlyIIRI1_IcaRA_module - 1 - - - - HlyIIR_protein - 1 - - - - - - - - - IcaRA - 1 - - - - - - - - - IcaRA_protein - 1 - - - - - - - - - pHlyIIR - 1 - - - - - - - - - I1_IcaRA_fc - 1 - - - - - - - IcaRA_mapsTo - 1 - - - - - - - - - - - tu_pHlyIIRI1_IcaRA_fc - 1 - - - - - - - I1_IcaRA_mapsTo - 1 - - - - - - - - - pHlyIIR_mapsTo - 1 - - - - - - - - - - - tu_pHlyIIRI1_IcaRA_module_IcaRA_protein_production_sub - 1 - - - - - tu_pHlyIIRI1_IcaRA_module_IcaRA_protein_production_sub_IcaRA_IcaRA - 1 - - - - - - - - - tu_pHlyIIRI1_IcaRA_module_IcaRA_protein_production_sub_IcaRA_protein_IcaRA_protein - 1 - - - - - - - - - - - tu_pHlyIIRI1_IcaRA_module_HlyIIR_pHlyIIR_repression_sub - 1 - - - - - tu_pHlyIIRI1_IcaRA_module_HlyIIR_pHlyIIR_repression_sub_pHlyIIR_pHlyIIR - 1 - - - - - - - - - tu_pHlyIIRI1_IcaRA_module_HlyIIR_pHlyIIR_repression_sub_HlyIIR_protein_HlyIIR_protein - 1 - - - - - - - - - - - tu_pHlyIIRI1_IcaRA_module_IcaRA_protein_degradation_sub - 1 - - - - - tu_pHlyIIRI1_IcaRA_module_IcaRA_protein_degradation_sub_IcaRA_protein_IcaRA_protein - 1 - - - - - - - - - - - tu_pHlyIIRI1_IcaRA_module_HlyIIR_protein_degradation_sub - 1 - - - - - tu_pHlyIIRI1_IcaRA_module_HlyIIR_protein_degradation_sub_HlyIIR_protein_HlyIIR_protein - 1 - - - - - - - - - - - HlyIIR_pHlyIIR_repression - 1 - - - - HlyIIR_protein - 1 - - - - - - - - - pHlyIIR - 1 - - - - - - - - - HlyIIR_pHlyIIR_repression - 1 - - - - - pHlyIIR_promoter_participation - 1 - - - - - - - - HlyIIR_protein_participation - 1 - - - - - - - - - - IcaRA_protein - 1 - IcaRA_protein - 2018-05-09T19:41:51.056Z - - - - - BetI_protein - 1 - BetI_protein - 2018-05-09T19:41:51.056Z - - - - - pHlyIIR - 1 - - pHlyIIR - 2018-05-09T19:41:51.056Z - - - - - - - - - E1_BetI - 1 - - E1_BetI - 2018-05-09T19:41:51.056Z - - - 5455A4 - 0.41 - TetR - NOR - BetI - 2.4 - ymin+(ymax-ymin)/(1.0+(x/K)^n) - 0.41646314 - 2.131948906 - 3.8 - 0.07 - - - - - - - - BetI - 1 - - - - - - - - - - RiboJ57 - 1 - - - - - - - - - - L3S3P11 - 1 - - - - - - - - - - E1 - 1 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 98 - 685 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 79 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 80 - 97 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 686 - 732 - - - - - - - - - - - AmeR_protein - 1 - AmeR_protein - 2018-05-09T19:41:51.056Z - - - - - pIcaRA - 1 - - pIcaRA - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pBM3R1F1_AmeR - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation - 1 - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation_Range - 1 - 1 - 66 - - - - - - - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation1 - 1 - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation1_Range - 1 - 67 - 887 - - - - - - - - - - tu_pBM3R1F1_AmeR_SequenceConstraint - 1 - - - - - - - - - - AmeR - 1 - - AmeR - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pBetIpIcaRAA1_AmtR - 1 - - - - - - - - Pro1_Component - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation2 - 1 - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation2_Range - 1 - 131 - 970 - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation - 1 - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation_Range - 1 - 1 - 63 - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation1 - 1 - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation1_Range - 1 - 64 - 130 - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceConstraint - 1 - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceConstraint1 - 1 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Pro1_Component - 1 - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation - 1 - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation_Range - 1 - 1 - 63 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation2 - 1 - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation2_Range - 1 - 127 - 858 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation1 - 1 - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation1_Range - 1 - 64 - 126 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceConstraint1 - 1 - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceConstraint - 1 - - - - - - - - - - AmtR_protein - 1 - AmtR_protein - 2018-05-09T19:41:51.056Z - - - - - A1 - 1 - - A1 - 2018-05-09T19:41:51.056Z - - - - - - - - - E1 - 1 - - E1 - 2018-05-09T19:41:51.056Z - - - - - - - - - pAmtR - 1 - - pAmtR - 2018-05-09T19:41:51.056Z - - - - - - - - - I1_IcaRA - 1 - - I1_IcaRA - 2018-05-09T19:41:51.056Z - - - E83C96 - 0.1 - TetR - NOR - IcaRA - 1.4 - ymin+(ymax-ymin)/(1.0+(x/K)^n) - 0.105541491 - 1.010814719 - 2.2 - 0.08 - - - - - - - - I1 - 1 - - - - - - - - - - IcaRA - 1 - - - - - - - - - - ECK120016170 - 1 - - - - - - - - - - ElvJ - 1 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 119 - 679 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 82 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 83 - 118 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 680 - 726 - - - - - - - - - - - ECK120016170 - 1 - - ECK120016170 - 2018-05-09T19:41:51.056Z - - - - - - - - - pBetI - 1 - - pBetI - 2018-05-09T19:41:51.056Z - - - - - - - - - HlyIIR_protein - 1 - HlyIIR_protein - 2018-05-09T19:41:51.056Z - - - - - RiboJ57 - 1 - - RiboJ57 - 2018-05-09T19:41:51.056Z - - - - - - - - - RiboJ54 - 1 - - RiboJ54 - 2018-05-09T19:41:51.056Z - - - - - - - - - BetI - 1 - - BetI - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pHlyIIRI1_IcaRA - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation1 - 1 - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation1_Range - 1 - 64 - 789 - - - - - - - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation - 1 - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation_Range - 1 - 1 - 63 - - - - - - - - - - tu_pHlyIIRI1_IcaRA_SequenceConstraint - 1 - - - - - - - - - - BydvJ - 1 - - BydvJ - 2018-05-09T19:41:51.056Z - - - - - - - - - IcaRA - 1 - - IcaRA - 2018-05-09T19:41:51.056Z - - - - - - - - - L3S2P55 - 1 - - L3S2P55 - 2018-05-09T19:41:51.056Z - - - - - - - - - pBM3R1 - 1 - - pBM3R1 - 2018-05-09T19:41:51.056Z - - - - - - - - - I1 - 1 - - I1 - 2018-05-09T19:41:51.056Z - - - - - - - - - BM3R1_protein - 1 - BM3R1_protein - 2018-05-09T19:41:51.056Z - - - - - L3S3P11 - 1 - - L3S3P11 - 2018-05-09T19:41:51.056Z - - - - - - - - - pAmeR - 1 - - pAmeR - 2018-05-09T19:41:51.056Z - - - - - - - - - AmtR - 1 - - AmtR - 2018-05-09T19:41:51.056Z - - - - - - - - - F1 - 1 - - F1 - 2018-05-09T19:41:51.056Z - - - - - - - - - F1_AmeR - 1 - - F1_AmeR - 2018-05-09T19:41:51.056Z - - - 6FCDE1 - 0.09 - TetR - NOR - AmeR - 1.4 - ymin+(ymax-ymin)/(1.0+(x/K)^n) - 0.097441924 - 0.680980375 - 3.8 - 0.2 - - - - - - - - AmeR - 1 - - - - - - - - - - L3S3P31 - 1 - - - - - - - - - - RiboJ54 - 1 - - - - - - - - - - F1 - 1 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 80 - 114 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 115 - 774 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 775 - 821 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 79 - - - - - - - - - - - A1_AmtR - 1 - - A1_AmtR - 2018-05-09T19:41:51.056Z - - - 3BA9E0 - 0.07 - TetR - NOR - AmtR - 1.6 - ymin+(ymax-ymin)/(1.0+(x/K)^n) - 0.071418036 - 0.917082477 - 3.8 - 0.06 - - - - - - - - A1 - 1 - - - - - - - - - - L3S2P55 - 1 - - - - - - - - - - BydvJ - 1 - - - - - - - - - - AmtR - 1 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 115 - 783 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 784 - 840 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 80 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 81 - 114 - - - - - - - - - - - L3S3P31 - 1 - - L3S3P31 - 2018-05-09T19:41:51.056Z - - - - - - - - - ElvJ - 1 - - ElvJ - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pAmeRpAmtRE1_BetISequence - 1 - - TCGTCACTAGAGGGCGATAGTGACAAACTTGACAACTCATCACTTCCTAGGTATAATGCTAGCCTTGTCCAACCAAATGATTCGTTACCAATTGACAGTTTCTATCGATCTATAGATAATGCTAGCCTGAAGAAGTCAATTAATGTGCTTTTAATTCTGATGAGTCGGTGACGACGAAACTTCCTCTACAAATAATTTTGTTTAACCCCCCGAGGAGTAGCACATGCCGAAACTGGGTATGCAGAGCATTCGTCGTCGTCAGCTGATTGATGCAACCCTGGAAGCAATTAATGAAGTTGGTATGCATGATGCAACCATTGCACAGATTGCACGTCGTGCCGGTGTTAGCACCGGTATTATTAGCCATTATTTCCGCGATAAAAACGGTCTGCTGGAAGCAACCATGCGTGATATTACCAGCCAGCTGCGTGATGCAGTTCTGAATCGTCTGCATGCACTGCCGCAGGGTAGCGCAGAACAGCGTCTGCAGGCAATTGTTGGTGGTAATTTTGATGAAACCCAGGTTAGCAGCGCAGCAATGAAAGCATGGCTGGCATTTTGGGCAAGCAGCATGCATCAGCCGATGCTGTATCGTCTGCAGCAGGTTAGCAGTCGTCGTCTGCTGAGCAATCTGGTTAGCGAATTTCGTCGTGAACTGCCTCGTGAACAGGCACAAGAGGCAGGTTATGGTCTGGCAGCACTGATTGATGGTCTGTGGCTGCGTGCAGCACTGAGCGGTAAACCGCTGGATAAAACCCGTGCAAATAGCCTGACCCGTCATTTTATCACCCAGCATCTGCCGACCGATTAACCAATTATTGAACACCCTTCGGGGTGTTTTTTTGTTTCTGGTCTACC - - - - - pHlyIIR_sequence - 1 - - pHlyIIR_sequence - 2018-05-09T19:41:51.056Z - - - ACCAGGAATCTGAACGATTCGTTACCAATTGACATATTTAAAATTCTTGTTTAAAatgctagc - - - - - F1_AmeR_sequence - 1 - - F1_AmeR_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGGGGTCAGTTGATGTGCTTTCAACTCTGATGAGTCAGTGATGACGAAACCCCCTCTACAAATAATTTTGTTTAACTATGGACTATGTTTTCACATACGAGGGGGATTAGATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAACCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC - - - - - ElvJ_sequence - 1 - - ElvJ_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaa - - - - - AmeR_sequence - 1 - - AmeR_sequence - 2018-05-09T19:41:51.056Z - - - ATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAA - - - - - pBM3R1_sequence - 1 - - pBM3R1_sequence - 2018-05-09T19:41:51.056Z - - - AATCCGCGTGATAGGTCTGATTCGTTACCAATTGACGGAATGAACGTTCATTCCGATAATGCTAGC - - - - - AmtR_sequence - 1 - - AmtR_sequence - 2018-05-09T19:41:51.056Z - - - ATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAA - - - - - ECK120016170_sequence - 1 - - ECK120016170_sequence - 2018-05-09T19:41:51.056Z - - - ACAATTTTCGAAAAAACCCGCTTCGGCGGGTTTTTTTATAGCTAAAA - - - - - BetI_sequence - 1 - - BetI_sequence - 2018-05-09T19:41:51.056Z - - - ATGCCGAAACTGGGTATGCAGAGCATTCGTCGTCGTCAGCTGATTGATGCAACCCTGGAAGCAATTAATGAAGTTGGTATGCATGATGCAACCATTGCACAGATTGCACGTCGTGCCGGTGTTAGCACCGGTATTATTAGCCATTATTTCCGCGATAAAAACGGTCTGCTGGAAGCAACCATGCGTGATATTACCAGCCAGCTGCGTGATGCAGTTCTGAATCGTCTGCATGCACTGCCGCAGGGTAGCGCAGAACAGCGTCTGCAGGCAATTGTTGGTGGTAATTTTGATGAAACCCAGGTTAGCAGCGCAGCAATGAAAGCATGGCTGGCATTTTGGGCAAGCAGCATGCATCAGCCGATGCTGTATCGTCTGCAGCAGGTTAGCAGTCGTCGTCTGCTGAGCAATCTGGTTAGCGAATTTCGTCGTGAACTGCCTCGTGAACAGGCACAAGAGGCAGGTTATGGTCTGGCAGCACTGATTGATGGTCTGTGGCTGCGTGCAGCACTGAGCGGTAAACCGCTGGATAAAACCCGTGCAAATAGCCTGACCCGTCATTTTATCACCCAGCATCTGCCGACCGATTAA - - - - - tu_pHlyIIRI1_IcaRASequence - 1 - - ACCAGGAATCTGAACGATTCGTTACCAATTGACATATTTAAAATTCTTGTTTAAAatgctagcCTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaaATTGCTATGGACTATGTTTCAAAGTGAGAATACTAGGTGAAAGACAAAATTATCGATAACGCCATCACCCTGTTTAGCGAAAAAGGTTATGACGGCACCACCCTGGATGATATTGCAAAAAGCGTGAACATCAAAAAAGCCAGCCTGTATTATCACTTTGATAGCAAAAAAAGCATCTACGAGCAGAGCGTTAAATGCTGTTTCGATTATCTGAACAACATCATCATGATGAACCAGAACAAAAGCAACTATAGCATCGATGCCCTGTATCAGTTTCTGTTTGAGTTCATCTTCGATATCGAGGAACGCTATATTCGTATGTATGTTCAGCTGAGCAACACACCGGAAGAATTTTCAGGTAACATTTATGGCCAGATCCAGGATCTGAATCAGAGCCTGAGCAAAGAAATCGCCAAATTCTATGACGAAAGCAAAATCAAAATGACCAAAGAGGACTTCCAGAATCTGATTCTGCTGTTTCTGGAAAGCTGGTATCTGAAAGCCAGCTTTAGCCAGAAATTTGGTGCAGTTGAAGAAAGCAAAAGCCAGTTTAAAGATGAGGTTTATAGCCTGCTGAACATCTTTCTGAAGAAATAAACAATTTTCGAAAAAACCCGCTTCGGCGGGTTTTTTTATAGCTAAAA - - - - - E1_BetI_sequence - 1 - - E1_BetI_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGAAGTCAATTAATGTGCTTTTAATTCTGATGAGTCGGTGACGACGAAACTTCCTCTACAAATAATTTTGTTTAACCCCCCGAGGAGTAGCACATGCCGAAACTGGGTATGCAGAGCATTCGTCGTCGTCAGCTGATTGATGCAACCCTGGAAGCAATTAATGAAGTTGGTATGCATGATGCAACCATTGCACAGATTGCACGTCGTGCCGGTGTTAGCACCGGTATTATTAGCCATTATTTCCGCGATAAAAACGGTCTGCTGGAAGCAACCATGCGTGATATTACCAGCCAGCTGCGTGATGCAGTTCTGAATCGTCTGCATGCACTGCCGCAGGGTAGCGCAGAACAGCGTCTGCAGGCAATTGTTGGTGGTAATTTTGATGAAACCCAGGTTAGCAGCGCAGCAATGAAAGCATGGCTGGCATTTTGGGCAAGCAGCATGCATCAGCCGATGCTGTATCGTCTGCAGCAGGTTAGCAGTCGTCGTCTGCTGAGCAATCTGGTTAGCGAATTTCGTCGTGAACTGCCTCGTGAACAGGCACAAGAGGCAGGTTATGGTCTGGCAGCACTGATTGATGGTCTGTGGCTGCGTGCAGCACTGAGCGGTAAACCGCTGGATAAAACCCGTGCAAATAGCCTGACCCGTCATTTTATCACCCAGCATCTGCCGACCGATTAACCAATTATTGAACACCCTTCGGGGTGTTTTTTTGTTTCTGGTCTACC - - - - - L3S2P55_sequence - 1 - - L3S2P55_sequence - 2018-05-09T19:41:51.056Z - - - CTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC - - - - - I1_IcaRA_sequence - 1 - - I1_IcaRA_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaaATTGCTATGGACTATGTTTCAAAGTGAGAATACTAGGTGAAAGACAAAATTATCGATAACGCCATCACCCTGTTTAGCGAAAAAGGTTATGACGGCACCACCCTGGATGATATTGCAAAAAGCGTGAACATCAAAAAAGCCAGCCTGTATTATCACTTTGATAGCAAAAAAAGCATCTACGAGCAGAGCGTTAAATGCTGTTTCGATTATCTGAACAACATCATCATGATGAACCAGAACAAAAGCAACTATAGCATCGATGCCCTGTATCAGTTTCTGTTTGAGTTCATCTTCGATATCGAGGAACGCTATATTCGTATGTATGTTCAGCTGAGCAACACACCGGAAGAATTTTCAGGTAACATTTATGGCCAGATCCAGGATCTGAATCAGAGCCTGAGCAAAGAAATCGCCAAATTCTATGACGAAAGCAAAATCAAAATGACCAAAGAGGACTTCCAGAATCTGATTCTGCTGTTTCTGGAAAGCTGGTATCTGAAAGCCAGCTTTAGCCAGAAATTTGGTGCAGTTGAAGAAAGCAAAAGCCAGTTTAAAGATGAGGTTTATAGCCTGCTGAACATCTTTCTGAAGAAATAAACAATTTTCGAAAAAACCCGCTTCGGCGGGTTTTTTTATAGCTAAAA - - - - - pBetI_sequence - 1 - - pBetI_sequence - 2018-05-09T19:41:51.056Z - - - AGCGCGGGTGAGAGGGATTCGTTACCAATTGACAATTGATTGGACGTTCAATATAATGCTAGC - - - - - tu_pBetIpIcaRAA1_AmtRSequence - 1 - - AGCGCGGGTGAGAGGGATTCGTTACCAATTGACAATTGATTGGACGTTCAATATAATGCTAGCGTCAACTCATAAGATtctgattcgttaccaattgacaaTTCACCTACCTTTCGTTAGgTTAGGTTGTCTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaaAATGTTCCCTAATAATCAGCAAAGAGGTTACTAGATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAACTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC - - - - - F1_sequence - 1 - - F1_sequence - 2018-05-09T19:41:51.056Z - - - CTATGGACTATGTTTTCACATACGAGGGGGATTAG - - - - - BydvJ_sequence - 1 - - BydvJ_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaa - - - - - pIcaRA_sequence - 1 - - pIcaRA_sequence - 2018-05-09T19:41:51.056Z - - - GTCAACTCATAAGATtctgattcgttaccaattgacaaTTCACCTACCTTTCGTTAGgTTAGGTTGT - - - - - pAmtR_sequence - 1 - - pAmtR_sequence - 2018-05-09T19:41:51.056Z - - - CTTGTCCAACCAAATGATTCGTTACCAATTGACAGTTTCTATCGATCTATAGATAATGCTAGC - - - - - E1_sequence - 1 - - E1_sequence - 2018-05-09T19:41:51.056Z - - - CCCCCCGAGGAGTAGCAC - - - - - L3S3P11_sequence - 1 - - L3S3P11_sequence - 2018-05-09T19:41:51.056Z - - - CCAATTATTGAACACCCTTCGGGGTGTTTTTTTGTTTCTGGTCTACC - - - - - pAmeR_sequence - 1 - - pAmeR_sequence - 2018-05-09T19:41:51.056Z - - - TCGTCACTAGAGGGCGATAGTGACAAACTTGACAACTCATCACTTCCTAGGTATAATGCTAGC - - - - - A1_sequence - 1 - - A1_sequence - 2018-05-09T19:41:51.056Z - - - AATGTTCCCTAATAATCAGCAAAGAGGTTACTAG - - - - - RiboJ54_sequence - 1 - - RiboJ54_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGGGGTCAGTTGATGTGCTTTCAACTCTGATGAGTCAGTGATGACGAAACCCCCTCTACAAATAATTTTGTTTAA - - - - - I1_sequence - 1 - - I1_sequence - 2018-05-09T19:41:51.056Z - - - ATTGCTATGGACTATGTTTCAAAGTGAGAATACTAG - - - - - A1_AmtR_sequence - 1 - - A1_AmtR_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaaAATGTTCCCTAATAATCAGCAAAGAGGTTACTAGATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAACTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC - - - - - IcaRA_sequence - 1 - - IcaRA_sequence - 2018-05-09T19:41:51.056Z - - - GTGAAAGACAAAATTATCGATAACGCCATCACCCTGTTTAGCGAAAAAGGTTATGACGGCACCACCCTGGATGATATTGCAAAAAGCGTGAACATCAAAAAAGCCAGCCTGTATTATCACTTTGATAGCAAAAAAAGCATCTACGAGCAGAGCGTTAAATGCTGTTTCGATTATCTGAACAACATCATCATGATGAACCAGAACAAAAGCAACTATAGCATCGATGCCCTGTATCAGTTTCTGTTTGAGTTCATCTTCGATATCGAGGAACGCTATATTCGTATGTATGTTCAGCTGAGCAACACACCGGAAGAATTTTCAGGTAACATTTATGGCCAGATCCAGGATCTGAATCAGAGCCTGAGCAAAGAAATCGCCAAATTCTATGACGAAAGCAAAATCAAAATGACCAAAGAGGACTTCCAGAATCTGATTCTGCTGTTTCTGGAAAGCTGGTATCTGAAAGCCAGCTTTAGCCAGAAATTTGGTGCAGTTGAAGAAAGCAAAAGCCAGTTTAAAGATGAGGTTTATAGCCTGCTGAACATCTTTCTGAAGAAATAA - - - - - L3S3P31_sequence - 1 - - L3S3P31_sequence - 2018-05-09T19:41:51.056Z - - - CCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC - - - - - RiboJ57_sequence - 1 - - RiboJ57_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGAAGTCAATTAATGTGCTTTTAATTCTGATGAGTCGGTGACGACGAAACTTCCTCTACAAATAATTTTGTTTAA - - - - - tu_pBM3R1F1_AmeRSequence - 1 - - AATCCGCGTGATAGGTCTGATTCGTTACCAATTGACGGAATGAACGTTCATTCCGATAATGCTAGCCTGAAGGGGTCAGTTGATGTGCTTTCAACTCTGATGAGTCAGTGATGACGAAACCCCCTCTACAAATAATTTTGTTTAACTATGGACTATGTTTTCACATACGAGGGGGATTAGATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAACCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC - - - - - tu_pBM3R1F1_AmeR_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-12T18:44:43.507-06:00 - - - - Association - 1 - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-12T13:14:31.817-06:00 - - - - Association - 1 - - - - - - - - tu_pAmeRpAmtRE1_BetI_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-11T18:31:13.311-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2sbol_Activity - 1 - Cello UCF to SBOL conversion - Conversion of the Cello UCF parts and metadata to SBOL 2 documents. - - - 2018-05-09T13:41:51.098-06:00 - - - - association - 1 - - - - - - - - - UCF_file - 1 - - - - - - - - - tu_pHlyIIRI1_IcaRA_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-12T19:01:23.171-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2SBOL - 1 - Cello UCF to SBOL - A script to convert Cello UCF parts and metadata to SBOL 2 documents. - - Chris J. 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- - - BetI - 1 - - - - - - - - - - RiboJ57 - 1 - - - - - - - - - - L3S3P11 - 1 - - - - - - - - - - E1 - 1 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 98 - 685 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 79 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 80 - 97 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 686 - 732 - - - - - - - - - - - AmeR_protein - 1 - AmeR_protein - 2018-05-09T19:41:51.056Z - - - - - pIcaRA - 1 - - pIcaRA - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pBM3R1F1_AmeR - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation - 1 - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation_Range - 1 - 1 - 66 - - - - - - - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation1 - 1 - - - - tu_pBM3R1F1_AmeR_SequenceAnnotation1_Range - 1 - 67 - 887 - - - - - - - - - - tu_pBM3R1F1_AmeR_SequenceConstraint - 1 - - - - - - - - - - AmeR - 1 - - AmeR - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pBetIpIcaRAA1_AmtR - 1 - - - - - - - - Pro1_Component - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation2 - 1 - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation2_Range - 1 - 131 - 970 - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation - 1 - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation_Range - 1 - 1 - 63 - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation1 - 1 - - - - tu_pBetIpIcaRAA1_AmtR_SequenceAnnotation1_Range - 1 - 64 - 130 - - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceConstraint - 1 - - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SequenceConstraint1 - 1 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Pro1_Component - 1 - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation - 1 - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation_Range - 1 - 1 - 63 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation2 - 1 - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation2_Range - 1 - 127 - 858 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation1 - 1 - - - - tu_pAmeRpAmtRE1_BetI_SequenceAnnotation1_Range - 1 - 64 - 126 - - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceConstraint1 - 1 - - - - - - - - - tu_pAmeRpAmtRE1_BetI_SequenceConstraint - 1 - - - - - - - - - - AmtR_protein - 1 - AmtR_protein - 2018-05-09T19:41:51.056Z - - - - - A1 - 1 - - A1 - 2018-05-09T19:41:51.056Z - - - - - - - - - E1 - 1 - - E1 - 2018-05-09T19:41:51.056Z - - - - - - - - - pAmtR - 1 - - pAmtR - 2018-05-09T19:41:51.056Z - - - - - - - - - I1_IcaRA - 1 - - I1_IcaRA - 2018-05-09T19:41:51.056Z - - - E83C96 - 0.1 - TetR - NOR - IcaRA - 1.4 - ymin+(ymax-ymin)/(1.0+(x/K)^n) - 0.105541491 - 1.010814719 - 2.2 - 0.08 - - - - - - - - I1 - 1 - - - - - - - - - - IcaRA - 1 - - - - - - - - - - ECK120016170 - 1 - - - - - - - - - - ElvJ - 1 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 119 - 679 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 82 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 83 - 118 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 680 - 726 - - - - - - - - - - - ECK120016170 - 1 - - ECK120016170 - 2018-05-09T19:41:51.056Z - - - - - - - - - pBetI - 1 - - pBetI - 2018-05-09T19:41:51.056Z - - - - - - - - - HlyIIR_protein - 1 - HlyIIR_protein - 2018-05-09T19:41:51.056Z - - - - - RiboJ57 - 1 - - RiboJ57 - 2018-05-09T19:41:51.056Z - - - - - - - - - RiboJ54 - 1 - - RiboJ54 - 2018-05-09T19:41:51.056Z - - - - - - - - - BetI - 1 - - BetI - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pHlyIIRI1_IcaRA - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Gen_Component - 1 - - - - - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation1 - 1 - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation1_Range - 1 - 64 - 789 - - - - - - - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation - 1 - - - - tu_pHlyIIRI1_IcaRA_SequenceAnnotation_Range - 1 - 1 - 63 - - - - - - - - - - tu_pHlyIIRI1_IcaRA_SequenceConstraint - 1 - - - - - - - - - - BydvJ - 1 - - BydvJ - 2018-05-09T19:41:51.056Z - - - - - - - - - IcaRA - 1 - - IcaRA - 2018-05-09T19:41:51.056Z - - - - - - - - - L3S2P55 - 1 - - L3S2P55 - 2018-05-09T19:41:51.056Z - - - - - - - - - pBM3R1 - 1 - - pBM3R1 - 2018-05-09T19:41:51.056Z - - - - - - - - - I1 - 1 - - I1 - 2018-05-09T19:41:51.056Z - - - - - - - - - BM3R1_protein - 1 - BM3R1_protein - 2018-05-09T19:41:51.056Z - - - - - L3S3P11 - 1 - - L3S3P11 - 2018-05-09T19:41:51.056Z - - - - - - - - - pAmeR - 1 - - pAmeR - 2018-05-09T19:41:51.056Z - - - - - - - - - AmtR - 1 - - AmtR - 2018-05-09T19:41:51.056Z - - - - - - - - - F1 - 1 - - F1 - 2018-05-09T19:41:51.056Z - - - - - - - - - F1_AmeR - 1 - - F1_AmeR - 2018-05-09T19:41:51.056Z - - - 6FCDE1 - 0.09 - TetR - NOR - AmeR - 1.4 - ymin+(ymax-ymin)/(1.0+(x/K)^n) - 0.097441924 - 0.680980375 - 3.8 - 0.2 - - - - - - - - AmeR - 1 - - - - - - - - - - L3S3P31 - 1 - - - - - - - - - - RiboJ54 - 1 - - - - - - - - - - F1 - 1 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 80 - 114 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 115 - 774 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 775 - 821 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 79 - - - - - - - - - - - A1_AmtR - 1 - - A1_AmtR - 2018-05-09T19:41:51.056Z - - - 3BA9E0 - 0.07 - TetR - NOR - AmtR - 1.6 - ymin+(ymax-ymin)/(1.0+(x/K)^n) - 0.071418036 - 0.917082477 - 3.8 - 0.06 - - - - - - - - A1 - 1 - - - - - - - - - - L3S2P55 - 1 - - - - - - - - - - BydvJ - 1 - - - - - - - - - - AmtR - 1 - - - - - - - - - - annotation2 - 1 - - - - - - range - 1 - - - 115 - 783 - - - - - - - - - - annotation3 - 1 - - - - - - range - 1 - - - 784 - 840 - - - - - - - - - - annotation0 - 1 - - - - - - range - 1 - - - 1 - 80 - - - - - - - - - - annotation1 - 1 - - - - - - range - 1 - - - 81 - 114 - - - - - - - - - - - L3S3P31 - 1 - - L3S3P31 - 2018-05-09T19:41:51.056Z - - - - - - - - - ElvJ - 1 - - ElvJ - 2018-05-09T19:41:51.056Z - - - - - - - - - tu_pAmeRpAmtRE1_BetISequence - 1 - - TCGTCACTAGAGGGCGATAGTGACAAACTTGACAACTCATCACTTCCTAGGTATAATGCTAGCCTTGTCCAACCAAATGATTCGTTACCAATTGACAGTTTCTATCGATCTATAGATAATGCTAGCCTGAAGAAGTCAATTAATGTGCTTTTAATTCTGATGAGTCGGTGACGACGAAACTTCCTCTACAAATAATTTTGTTTAACCCCCCGAGGAGTAGCACATGCCGAAACTGGGTATGCAGAGCATTCGTCGTCGTCAGCTGATTGATGCAACCCTGGAAGCAATTAATGAAGTTGGTATGCATGATGCAACCATTGCACAGATTGCACGTCGTGCCGGTGTTAGCACCGGTATTATTAGCCATTATTTCCGCGATAAAAACGGTCTGCTGGAAGCAACCATGCGTGATATTACCAGCCAGCTGCGTGATGCAGTTCTGAATCGTCTGCATGCACTGCCGCAGGGTAGCGCAGAACAGCGTCTGCAGGCAATTGTTGGTGGTAATTTTGATGAAACCCAGGTTAGCAGCGCAGCAATGAAAGCATGGCTGGCATTTTGGGCAAGCAGCATGCATCAGCCGATGCTGTATCGTCTGCAGCAGGTTAGCAGTCGTCGTCTGCTGAGCAATCTGGTTAGCGAATTTCGTCGTGAACTGCCTCGTGAACAGGCACAAGAGGCAGGTTATGGTCTGGCAGCACTGATTGATGGTCTGTGGCTGCGTGCAGCACTGAGCGGTAAACCGCTGGATAAAACCCGTGCAAATAGCCTGACCCGTCATTTTATCACCCAGCATCTGCCGACCGATTAACCAATTATTGAACACCCTTCGGGGTGTTTTTTTGTTTCTGGTCTACC - - - - - pHlyIIR_sequence - 1 - - pHlyIIR_sequence - 2018-05-09T19:41:51.056Z - - - ACCAGGAATCTGAACGATTCGTTACCAATTGACATATTTAAAATTCTTGTTTAAAatgctagc - - - - - F1_AmeR_sequence - 1 - - F1_AmeR_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGGGGTCAGTTGATGTGCTTTCAACTCTGATGAGTCAGTGATGACGAAACCCCCTCTACAAATAATTTTGTTTAACTATGGACTATGTTTTCACATACGAGGGGGATTAGATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAACCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC - - - - - ElvJ_sequence - 1 - - ElvJ_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaa - - - - - AmeR_sequence - 1 - - AmeR_sequence - 2018-05-09T19:41:51.056Z - - - ATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAA - - - - - pBM3R1_sequence - 1 - - pBM3R1_sequence - 2018-05-09T19:41:51.056Z - - - AATCCGCGTGATAGGTCTGATTCGTTACCAATTGACGGAATGAACGTTCATTCCGATAATGCTAGC - - - - - AmtR_sequence - 1 - - AmtR_sequence - 2018-05-09T19:41:51.056Z - - - ATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAA - - - - - ECK120016170_sequence - 1 - - ECK120016170_sequence - 2018-05-09T19:41:51.056Z - - - ACAATTTTCGAAAAAACCCGCTTCGGCGGGTTTTTTTATAGCTAAAA - - - - - BetI_sequence - 1 - - BetI_sequence - 2018-05-09T19:41:51.056Z - - - ATGCCGAAACTGGGTATGCAGAGCATTCGTCGTCGTCAGCTGATTGATGCAACCCTGGAAGCAATTAATGAAGTTGGTATGCATGATGCAACCATTGCACAGATTGCACGTCGTGCCGGTGTTAGCACCGGTATTATTAGCCATTATTTCCGCGATAAAAACGGTCTGCTGGAAGCAACCATGCGTGATATTACCAGCCAGCTGCGTGATGCAGTTCTGAATCGTCTGCATGCACTGCCGCAGGGTAGCGCAGAACAGCGTCTGCAGGCAATTGTTGGTGGTAATTTTGATGAAACCCAGGTTAGCAGCGCAGCAATGAAAGCATGGCTGGCATTTTGGGCAAGCAGCATGCATCAGCCGATGCTGTATCGTCTGCAGCAGGTTAGCAGTCGTCGTCTGCTGAGCAATCTGGTTAGCGAATTTCGTCGTGAACTGCCTCGTGAACAGGCACAAGAGGCAGGTTATGGTCTGGCAGCACTGATTGATGGTCTGTGGCTGCGTGCAGCACTGAGCGGTAAACCGCTGGATAAAACCCGTGCAAATAGCCTGACCCGTCATTTTATCACCCAGCATCTGCCGACCGATTAA - - - - - tu_pHlyIIRI1_IcaRASequence - 1 - - ACCAGGAATCTGAACGATTCGTTACCAATTGACATATTTAAAATTCTTGTTTAAAatgctagcCTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaaATTGCTATGGACTATGTTTCAAAGTGAGAATACTAGGTGAAAGACAAAATTATCGATAACGCCATCACCCTGTTTAGCGAAAAAGGTTATGACGGCACCACCCTGGATGATATTGCAAAAAGCGTGAACATCAAAAAAGCCAGCCTGTATTATCACTTTGATAGCAAAAAAAGCATCTACGAGCAGAGCGTTAAATGCTGTTTCGATTATCTGAACAACATCATCATGATGAACCAGAACAAAAGCAACTATAGCATCGATGCCCTGTATCAGTTTCTGTTTGAGTTCATCTTCGATATCGAGGAACGCTATATTCGTATGTATGTTCAGCTGAGCAACACACCGGAAGAATTTTCAGGTAACATTTATGGCCAGATCCAGGATCTGAATCAGAGCCTGAGCAAAGAAATCGCCAAATTCTATGACGAAAGCAAAATCAAAATGACCAAAGAGGACTTCCAGAATCTGATTCTGCTGTTTCTGGAAAGCTGGTATCTGAAAGCCAGCTTTAGCCAGAAATTTGGTGCAGTTGAAGAAAGCAAAAGCCAGTTTAAAGATGAGGTTTATAGCCTGCTGAACATCTTTCTGAAGAAATAAACAATTTTCGAAAAAACCCGCTTCGGCGGGTTTTTTTATAGCTAAAA - - - - - E1_BetI_sequence - 1 - - E1_BetI_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGAAGTCAATTAATGTGCTTTTAATTCTGATGAGTCGGTGACGACGAAACTTCCTCTACAAATAATTTTGTTTAACCCCCCGAGGAGTAGCACATGCCGAAACTGGGTATGCAGAGCATTCGTCGTCGTCAGCTGATTGATGCAACCCTGGAAGCAATTAATGAAGTTGGTATGCATGATGCAACCATTGCACAGATTGCACGTCGTGCCGGTGTTAGCACCGGTATTATTAGCCATTATTTCCGCGATAAAAACGGTCTGCTGGAAGCAACCATGCGTGATATTACCAGCCAGCTGCGTGATGCAGTTCTGAATCGTCTGCATGCACTGCCGCAGGGTAGCGCAGAACAGCGTCTGCAGGCAATTGTTGGTGGTAATTTTGATGAAACCCAGGTTAGCAGCGCAGCAATGAAAGCATGGCTGGCATTTTGGGCAAGCAGCATGCATCAGCCGATGCTGTATCGTCTGCAGCAGGTTAGCAGTCGTCGTCTGCTGAGCAATCTGGTTAGCGAATTTCGTCGTGAACTGCCTCGTGAACAGGCACAAGAGGCAGGTTATGGTCTGGCAGCACTGATTGATGGTCTGTGGCTGCGTGCAGCACTGAGCGGTAAACCGCTGGATAAAACCCGTGCAAATAGCCTGACCCGTCATTTTATCACCCAGCATCTGCCGACCGATTAACCAATTATTGAACACCCTTCGGGGTGTTTTTTTGTTTCTGGTCTACC - - - - - L3S2P55_sequence - 1 - - L3S2P55_sequence - 2018-05-09T19:41:51.056Z - - - CTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC - - - - - I1_IcaRA_sequence - 1 - - I1_IcaRA_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaaATTGCTATGGACTATGTTTCAAAGTGAGAATACTAGGTGAAAGACAAAATTATCGATAACGCCATCACCCTGTTTAGCGAAAAAGGTTATGACGGCACCACCCTGGATGATATTGCAAAAAGCGTGAACATCAAAAAAGCCAGCCTGTATTATCACTTTGATAGCAAAAAAAGCATCTACGAGCAGAGCGTTAAATGCTGTTTCGATTATCTGAACAACATCATCATGATGAACCAGAACAAAAGCAACTATAGCATCGATGCCCTGTATCAGTTTCTGTTTGAGTTCATCTTCGATATCGAGGAACGCTATATTCGTATGTATGTTCAGCTGAGCAACACACCGGAAGAATTTTCAGGTAACATTTATGGCCAGATCCAGGATCTGAATCAGAGCCTGAGCAAAGAAATCGCCAAATTCTATGACGAAAGCAAAATCAAAATGACCAAAGAGGACTTCCAGAATCTGATTCTGCTGTTTCTGGAAAGCTGGTATCTGAAAGCCAGCTTTAGCCAGAAATTTGGTGCAGTTGAAGAAAGCAAAAGCCAGTTTAAAGATGAGGTTTATAGCCTGCTGAACATCTTTCTGAAGAAATAAACAATTTTCGAAAAAACCCGCTTCGGCGGGTTTTTTTATAGCTAAAA - - - - - pBetI_sequence - 1 - - pBetI_sequence - 2018-05-09T19:41:51.056Z - - - AGCGCGGGTGAGAGGGATTCGTTACCAATTGACAATTGATTGGACGTTCAATATAATGCTAGC - - - - - tu_pBetIpIcaRAA1_AmtRSequence - 1 - - AGCGCGGGTGAGAGGGATTCGTTACCAATTGACAATTGATTGGACGTTCAATATAATGCTAGCGTCAACTCATAAGATtctgattcgttaccaattgacaaTTCACCTACCTTTCGTTAGgTTAGGTTGTCTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaaAATGTTCCCTAATAATCAGCAAAGAGGTTACTAGATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAACTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC - - - - - F1_sequence - 1 - - F1_sequence - 2018-05-09T19:41:51.056Z - - - CTATGGACTATGTTTTCACATACGAGGGGGATTAG - - - - - BydvJ_sequence - 1 - - BydvJ_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaa - - - - - pIcaRA_sequence - 1 - - pIcaRA_sequence - 2018-05-09T19:41:51.056Z - - - GTCAACTCATAAGATtctgattcgttaccaattgacaaTTCACCTACCTTTCGTTAGgTTAGGTTGT - - - - - pAmtR_sequence - 1 - - pAmtR_sequence - 2018-05-09T19:41:51.056Z - - - CTTGTCCAACCAAATGATTCGTTACCAATTGACAGTTTCTATCGATCTATAGATAATGCTAGC - - - - - E1_sequence - 1 - - E1_sequence - 2018-05-09T19:41:51.056Z - - - CCCCCCGAGGAGTAGCAC - - - - - L3S3P11_sequence - 1 - - L3S3P11_sequence - 2018-05-09T19:41:51.056Z - - - CCAATTATTGAACACCCTTCGGGGTGTTTTTTTGTTTCTGGTCTACC - - - - - pAmeR_sequence - 1 - - pAmeR_sequence - 2018-05-09T19:41:51.056Z - - - TCGTCACTAGAGGGCGATAGTGACAAACTTGACAACTCATCACTTCCTAGGTATAATGCTAGC - - - - - A1_sequence - 1 - - A1_sequence - 2018-05-09T19:41:51.056Z - - - AATGTTCCCTAATAATCAGCAAAGAGGTTACTAG - - - - - RiboJ54_sequence - 1 - - RiboJ54_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGGGGTCAGTTGATGTGCTTTCAACTCTGATGAGTCAGTGATGACGAAACCCCCTCTACAAATAATTTTGTTTAA - - - - - I1_sequence - 1 - - I1_sequence - 2018-05-09T19:41:51.056Z - - - ATTGCTATGGACTATGTTTCAAAGTGAGAATACTAG - - - - - A1_AmtR_sequence - 1 - - A1_AmtR_sequence - 2018-05-09T19:41:51.056Z - - - CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaaAATGTTCCCTAATAATCAGCAAAGAGGTTACTAGATGGCAGGCGCAGTTGGTCGTCCGCGTCGTAGTGCACCGCGTCGTGCAGGTAAAAATCCGCGTGAAGAAATTCTGGATGCAAGCGCAGAACTGTTTACCCGTCAGGGTTTTGCAACCACCAGTACCCATCAGATTGCAGATGCAGTTGGTATTCGTCAGGCAAGCCTGTATTATCATTTTCCGAGCAAAACCGAAATCTTTCTGACCCTGCTGAAAAGCACCGTTGAACCGAGCACCGTTCTGGCAGAAGATCTGAGCACCCTGGATGCAGGTCCGGAAATGCGTCTGTGGGCAATTGTTGCAAGCGAAGTTCGTCTGCTGCTGAGCACCAAATGGAATGTTGGTCGTCTGTATCAGCTGCCGATTGTTGGTAGCGAAGAATTTGCAGAATATCATAGCCAGCGTGAAGCACTGACCAATGTTTTTCGTGATCTGGCAACCGAAATTGTTGGTGATGATCCGCGTGCAGAACTGCCGTTTCATATTACCATGAGCGTTATTGAAATGCGTCGCAATGATGGTAAAATTCCGAGTCCGCTGAGCGCAGATAGCCTGCCGGAAACCGCAATTATGCTGGCAGATGCAAGCCTGGCAGTTCTGGGTGCACCGCTGCCTGCAGATCGTGTTGAAAAAACCCTGGAACTGATTAAACAGGCAGATGCAAAATAACTCGGTACCAAAGACGAACAATAAGACGCTGAAAAGCGTCTTTTTTCGTTTTGGTCC - - - - - IcaRA_sequence - 1 - - IcaRA_sequence - 2018-05-09T19:41:51.056Z - - - GTGAAAGACAAAATTATCGATAACGCCATCACCCTGTTTAGCGAAAAAGGTTATGACGGCACCACCCTGGATGATATTGCAAAAAGCGTGAACATCAAAAAAGCCAGCCTGTATTATCACTTTGATAGCAAAAAAAGCATCTACGAGCAGAGCGTTAAATGCTGTTTCGATTATCTGAACAACATCATCATGATGAACCAGAACAAAAGCAACTATAGCATCGATGCCCTGTATCAGTTTCTGTTTGAGTTCATCTTCGATATCGAGGAACGCTATATTCGTATGTATGTTCAGCTGAGCAACACACCGGAAGAATTTTCAGGTAACATTTATGGCCAGATCCAGGATCTGAATCAGAGCCTGAGCAAAGAAATCGCCAAATTCTATGACGAAAGCAAAATCAAAATGACCAAAGAGGACTTCCAGAATCTGATTCTGCTGTTTCTGGAAAGCTGGTATCTGAAAGCCAGCTTTAGCCAGAAATTTGGTGCAGTTGAAGAAAGCAAAAGCCAGTTTAAAGATGAGGTTTATAGCCTGCTGAACATCTTTCTGAAGAAATAA - - - - - L3S3P31_sequence - 1 - - L3S3P31_sequence - 2018-05-09T19:41:51.056Z - - - CCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC - - - - - RiboJ57_sequence - 1 - - RiboJ57_sequence - 2018-05-09T19:41:51.056Z - - - CTGAAGAAGTCAATTAATGTGCTTTTAATTCTGATGAGTCGGTGACGACGAAACTTCCTCTACAAATAATTTTGTTTAA - - - - - tu_pBM3R1F1_AmeRSequence - 1 - - AATCCGCGTGATAGGTCTGATTCGTTACCAATTGACGGAATGAACGTTCATTCCGATAATGCTAGCCTGAAGGGGTCAGTTGATGTGCTTTCAACTCTGATGAGTCAGTGATGACGAAACCCCCTCTACAAATAATTTTGTTTAACTATGGACTATGTTTTCACATACGAGGGGGATTAGATGAACAAAACCATTGATCAGGTGCGTAAAGGTGATCGTAAAAGCGATCTGCCGGTTCGTCGTCGTCCGCGTCGTAGTGCCGAAGAAACCCGTCGTGATATTCTGGCAAAAGCCGAAGAACTGTTTCGTGAACGTGGTTTTAATGCAGTTGCCATTGCAGATATTGCAAGCGCACTGAATATGAGTCCGGCAAATGTGTTTAAACATTTTAGCAGCAAAAACGCACTGGTTGATGCAATTGGTTTTGGTCAGATTGGTGTTTTTGAACGTCAGATTTGTCCGCTGGATAAAAGCCATGCACCGCTGGATCGTCTGCGTCATCTGGCACGTAATCTGATGGAACAGCATCATCAGGATCATTTCAAACACATACGGGTTTTTATTCAGATCCTGATGACCGCCAAACAGGATATGAAATGTGGCGATTATTACAAAAGCGTGATTGCAAAACTGCTGGCCGAAATTATTCGTGATGGTGTTGAAGCAGGTCTGTATATTGCAACCGATATTCCGGTTCTGGCAGAAACCGTTCTGCATGCACTGACCAGCGTTATTCATCCGGTTCTGATTGCACAAGAAGATATTGGTAATCTGGCAACCCGTTGTGATCAGCTGGTTGATCTGATTGATGCAGGTCTGCGTAATCCGCTGGCAAAATAACCAATTATTGAACACCCTAACGGGTGTTTTTTTTTTTTTGGTCTACC - - - - - tu_pBM3R1F1_AmeR_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-12T18:44:43.507-06:00 - - - - Association - 1 - - - - - - - - tu_pBetIpIcaRAA1_AmtR_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-12T13:14:31.817-06:00 - - - - Association - 1 - - - - - - - - tu_pAmeRpAmtRE1_BetI_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-11T18:31:13.311-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2sbol_Activity - 1 - Cello UCF to SBOL conversion - Conversion of the Cello UCF parts and metadata to SBOL 2 documents. - - - 2018-05-09T13:41:51.098-06:00 - - - - association - 1 - - - - - - - - - UCF_file - 1 - - - - - - - - - tu_pHlyIIRI1_IcaRA_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-08-12T19:01:23.171-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2SBOL - 1 - Cello UCF to SBOL - A script to convert Cello UCF parts and metadata to SBOL 2 documents. - - Chris J. 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- CD4__1_ - 1.0 - - - - - CD8_terminator - 1.0 - - - - - - CD14_promoter - 1.0 - - - - - - CD11_cds - 1.0 - - - - - - CD16_terminator - 1.0 - - - - - - CD0_r - 1.0 - - - - - CD10_promoter - 1.0 - - - - - - CD9_er - 1.0 - - - - - - C3_part - 1.0 - - - - - - - - C5_part - 1.0 - - - - - - - - C4_part - 1.0 - - - - - - \ No newline at end of file diff --git a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution.xml b/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution.xml deleted file mode 100644 index 937999bdd..000000000 --- a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution.xml +++ /dev/null @@ -1,2685 +0,0 @@ - - - - - LacI_protein_degradation - 1 - - - - LacI_protein - 1 - - - - - - - - - LacI_degradation_interaction - 1 - - - - - LacI_protein - 1 - - - - - - - - - - aTc_TetR_protein_degradation - 1 - - - - aTc_TetR_protein - 1 - - - - - - - - - aTc_TetR_protein_degradation_interaction - 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1 - - - - - - - - - Cello_ecoli_tuLacI_module_LacI_protein_production_sub_LacI_LacI - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub - 1 - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub_pTet_pTet - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - IPTG_LacI_protein_degradation - 1 - - - - IPTG_LacI_protein - 1 - - - - - - - - - IPTG_LacI_protein_degradation_interaction - 1 - - - - - IPTG_LacI_protein - 1 - - - - - - - - - - Cello_ecoli_tuTetR_module - 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- - - - Cello_ecoli_tuTetR_module_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_LacI_protein_degradation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_degradation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub - 1 - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub_pTac_pTac - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_aTc_aTc - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - TetR_protein_pTet_repression - 1 - - - - pTet - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - TetR_protein_pTet_repression - 1 - 0.0013 - 4.4 - - - - - pTet_promoter_participation - 1 - - - - - - - - TetR_protein_participation - 1 - - - - - - - - - - Cello_ecoli_tuYFP_module - 1 - - - - pTac - 1 - - - - - - - - - LacI_protein - 1 - - - - - - - - - YFP - 1 - - - - - - - - - Cello_ecoli_tuYFP_fc - 1 - - - - - - - pTac_mapsTo - 1 - - - - - - - - - YFP_mapsTo - 1 - - - - - - - - - - - IPTG_LacI_protein - 1 - - - - - - - - - IPTG - 1 - - - - - - - - - YFP_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_LacI_protein_degradation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_LacI_protein_pTac_repression_sub - 1 - - - - - Cello_ecoli_tuYFP_module_LacI_protein_pTac_repression_sub_pTac_pTac - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_LacI_protein_pTac_repression_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_YFP_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_YFP_protein_degradation_sub_YFP_protein_YFP_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_YFP_protein_production_sub - 1 - - - - - Cello_ecoli_tuYFP_module_YFP_protein_production_sub_YFP_protein_YFP_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_YFP_protein_production_sub_YFP_YFP - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_degradation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - - - TetR_protein_production - 1 - - - - TetR - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - TetR_protein_interaction - 1 - - - - - TetR - 1 - - - - - - - - TetR_protein - 1 - - - - - - - - - - LacI_protein_pTac_repression - 1 - - - - LacI_protein - 1 - - - - - - - - - pTac - 1 - - - - - - - - - LacI_protein_pTac_repression - 1 - 0.0034 - 2.8 - - - - - LacI_protein_participation - 1 - - - - - - - - pTac_promoter_participation - 1 - - - - - - - - - - LacI_protein_production - 1 - - - - LacI - 1 - - - - - - - - - LacI_protein - 1 - - - - - - - - - LacI_protein_interaction - 1 - - - - - LacI_protein - 1 - - - - - - - - LacI - 1 - - - - - - - - - - YFP_protein_degradation - 1 - - - - YFP_protein - 1 - - - - - - - - - YFP_degradation_interaction - 1 - - - - - YFP_protein - 1 - - - - - - - - - - aTc_TetR_protein_complex_formation - 1 - - - - aTc_TetR_protein - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - aTc - 1 - - - - - - - - - aTc_TetR_protein_complex_formation - 1 - - - - - TetR_protein - 1 - - - - - - - - aTc_TetR_protein - 1 - - - - - - - - aTc - 1 - - - - - - - - - - pTac - 1 - - pTac - 2019-02-20T23:57:58.276Z - - - - - - - - - TetR_protein - 1 - TetR_protein - 2019-02-20T23:57:58.276Z - - - - - ElvJ - 1 - - ElvJ - 2019-02-20T23:57:58.276Z - - - - - - - - - B2 - 1 - - B2 - 2019-02-20T23:57:58.276Z - - - - - - - - - ECK120010876 - 1 - - ECK120010876 - 2019-02-20T23:57:58.276Z - - - - - - - - - Q2 - 1 - - Q2 - 2019-02-20T23:57:58.276Z - - - - - - - - - aTc - 1 - - - - - ECK120015440 - 1 - - ECK120015440 - 2019-02-20T23:57:58.276Z - - - - - - - - - BydvJ - 1 - - BydvJ - 2019-02-20T23:57:58.276Z - - - - - - - - - YFP - 1 - - YFP - 2019-02-20T23:57:58.276Z - - - - - - - - - LacI - 1 - - LacI - 2019-02-20T23:57:58.276Z - - - - - - - - - ECK120010818 - 1 - - ECK120010818 - 2019-02-20T23:57:58.276Z - - - - - - - - - IPTG_LacI_protein - 1 - IPTG_LacI_protein - 2019-02-20T23:57:58.276Z - - - - - aTc_TetR_protein - 1 - aTc_TetR_protein - 2019-02-20T23:57:58.276Z - - - - - YFP_protein - 1 - YFP_protein - 2019-02-20T23:57:58.276Z - - - - - Cello_ecoli_tuTetR - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation2_Range - 1 - 154 - 190 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation_Range - 1 - 1 - 71 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation1_Range - 1 - 72 - 153 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation4_Range - 1 - 815 - 869 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation3_Range - 1 - 191 - 814 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint2 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint - 1 - - - - - - - - - - Cello_ecoli_tuYFP - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation2_Range - 1 - 157 - 193 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation4_Range - 1 - 1080 - 1128 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation3_Range - 1 - 194 - 1079 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation_Range - 1 - 1 - 71 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation1_Range - 1 - 72 - 156 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint2 - 1 - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint - 1 - - - - - - - - - - pTet - 1 - - pTet - 2019-02-20T23:57:58.276Z - - - - - - - - - LacI_protein - 1 - LacI_protein - 2019-02-20T23:57:58.276Z - - - - - TetR - 1 - - TetR - 2019-02-20T23:57:58.276Z - - - - - - - - - IPTG - 1 - - - - - PlmJ - 1 - - PlmJ - 2019-02-20T23:57:58.276Z - - - - - - - - - Cello_ecoli_tuLacI - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation4_Range - 1 - 1250 - 1303 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation3_Range - 1 - 164 - 1249 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation2_Range - 1 - 155 - 163 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation1_Range - 1 - 75 - 154 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation_Range - 1 - 1 - 74 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint2 - 1 - - - - - - - - - - H1 - 1 - - H1 - 2019-02-20T23:57:58.276Z - - - - - - - - - B2_sequence - 1 - - B2_sequence - 2019-02-20T23:57:58.276Z - - - CTATGGACTATGTTTTTCAAAGACGAAAAACTACTAG - - - - - H1_sequence - 1 - - H1_sequence - 2019-02-20T23:57:58.276Z - - - ACCCCCGAG - - - - - Cello_ecoli_tuLacISequence - 1 - - TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCACCTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaaACCCCCGAGatgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaggacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagatagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgccagtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgataaGTCAGTTTCACCTGTTTTACGTAAAAACCCGCTTCGGCGGGTTTTTACTTTTGG - - - - - ECK120010876_sequence - 1 - - ECK120010876_sequence - 2019-02-20T23:57:58.276Z - - - taaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta - - - - - BydvJ_sequence - 1 - - BydvJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaa - - - - - pTac_sequence - 1 - - pTac_sequence - 2019-02-20T23:57:58.276Z - - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATT - - - - - PlmJ_sequence - 1 - - PlmJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAAGTCATAAGTCTGGGCTAAGCCCACTGATGAGTCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAA - - - - - Cello_ecoli_tuYFPSequence - 1 - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATTCTGAAGTCATAAGTCTGGGCTAAGCCCACTGATGAGTCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAACTATGGACTATGTTTTTCAAAGACGAAAAACTACTAGCTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCCtccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca - - - - - LacI_sequence - 1 - - LacI_sequence - 2019-02-20T23:57:58.276Z - - - atgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaggacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagatagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgccagtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgataa - - - - - ECK120015440_sequence - 1 - - ECK120015440_sequence - 2019-02-20T23:57:58.276Z - - - tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca - - - - - Cello_ecoli_tuTetRSequence - 1 - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATTCTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaaGCCATGCCATTGGCTTTTGATAGAGGACAACTACTAGatgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtcctaataaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta - - - - - pTet_sequence - 1 - - pTet_sequence - 2019-02-20T23:57:58.276Z - - - TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCAC - - - - - TetR_sequence - 1 - - TetR_sequence - 2019-02-20T23:57:58.276Z - - - atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtcctaa - - - - - YFP_sequence - 1 - - YFP_sequence - 2019-02-20T23:57:58.276Z - - - CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC - - - - - ElvJ_sequence - 1 - - ElvJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaa - - - - - ECK120010818_sequence - 1 - - ECK120010818_sequence - 2019-02-20T23:57:58.276Z - - - GTCAGTTTCACCTGTTTTACGTAAAAACCCGCTTCGGCGGGTTTTTACTTTTGG - - - - - Q2_sequence - 1 - - Q2_sequence - 2019-02-20T23:57:58.276Z - - - GCCATGCCATTGGCTTTTGATAGAGGACAACTACTAG - - - - - Cello_ecoli_tuYFP_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-17T00:14:44.679-06:00 - - - - Association - 1 - - - - - - - - Cello_ecoli_tuTetR_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-17T00:05:08.085-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2sbol_Activity - 1 - Cello UCF to SBOL conversion - Conversion of the Cello UCF parts and metadata to SBOL 2 documents. - - - 2019-02-20T16:57:58.314-07:00 - - - - association - 1 - - - - - - - - - UCF_file - 1 - - - - - - - - - Cello_ecoli_tuLacI_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-16T23:55:58.519-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2SBOL - 1 - Cello UCF to SBOL - A script to convert Cello UCF parts and metadata to SBOL 2 documents. - - Prashant Vaidyanathan - Chris J. Myers - - - - - - attachment_00009g2fklS69eiQUeolIu - 1 - Eco1C1G1T1-synbiohub.UCF.json - - - - - 3570439 - 57292cc1b8f9be5abbc7a6e6824fdba12f35fb18 - - \ No newline at end of file diff --git a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution1.xml b/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution1.xml deleted file mode 100644 index 937999bdd..000000000 --- a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution1.xml +++ /dev/null @@ -1,2685 +0,0 @@ - - - - - LacI_protein_degradation - 1 - - - - LacI_protein - 1 - - - - - - - - - LacI_degradation_interaction - 1 - - - - - LacI_protein - 1 - - - - - - - - - - aTc_TetR_protein_degradation - 1 - - - - aTc_TetR_protein - 1 - - - - - - - - - aTc_TetR_protein_degradation_interaction - 1 - - - - - aTc_TetR_protein - 1 - - - - - - - - - - r_s_q_net - 1.0 - - - - FC0_LacI_protein - 1.0 - - - - - - - - - FC4_aTc - 1.0 - - - - - - - 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1 - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub_pTet_pTet - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - IPTG_LacI_protein_degradation - 1 - - - - IPTG_LacI_protein - 1 - - - - - - - - - IPTG_LacI_protein_degradation_interaction - 1 - - - - - IPTG_LacI_protein - 1 - - - - - - - - - - Cello_ecoli_tuTetR_module - 1 - - - - IPTG - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - IPTG_LacI_protein - 1 - - - - - - - - - aTc_TetR_protein - 1 - - - - - - - - - TetR - 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1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_degradation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub - 1 - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub_pTac_pTac - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_aTc_aTc - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - TetR_protein_pTet_repression - 1 - - - - pTet - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - TetR_protein_pTet_repression - 1 - 0.0013 - 4.4 - - - - - pTet_promoter_participation - 1 - - - - - - - - TetR_protein_participation - 1 - - - - - - - - - - Cello_ecoli_tuYFP_module - 1 - - - - pTac - 1 - - - - - - - - - LacI_protein - 1 - - - - - - - - - YFP - 1 - - - - - - - - - Cello_ecoli_tuYFP_fc - 1 - - - - - - - pTac_mapsTo - 1 - - - - - - - - - YFP_mapsTo - 1 - - - - - - - - - - - IPTG_LacI_protein - 1 - - - - - - - - - IPTG - 1 - - - - - - - - - YFP_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_LacI_protein_degradation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_LacI_protein_pTac_repression_sub - 1 - - - - - Cello_ecoli_tuYFP_module_LacI_protein_pTac_repression_sub_pTac_pTac - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_LacI_protein_pTac_repression_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_YFP_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_YFP_protein_degradation_sub_YFP_protein_YFP_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_YFP_protein_production_sub - 1 - - - - - Cello_ecoli_tuYFP_module_YFP_protein_production_sub_YFP_protein_YFP_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP_module_YFP_protein_production_sub_YFP_YFP - 1 - - - - - - - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP_module_IPTG_LacI_protein_degradation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - - - TetR_protein_production - 1 - - - - TetR - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - TetR_protein_interaction - 1 - - - - - TetR - 1 - - - - - - - - TetR_protein - 1 - - - - - - - - - - LacI_protein_pTac_repression - 1 - - - - LacI_protein - 1 - - - - - - - - - pTac - 1 - - - - - - - - - LacI_protein_pTac_repression - 1 - 0.0034 - 2.8 - - - - - LacI_protein_participation - 1 - - - - - - - - pTac_promoter_participation - 1 - - - - - - - - - - LacI_protein_production - 1 - - - - LacI - 1 - - - - - - - - - LacI_protein - 1 - - - - - - - - - LacI_protein_interaction - 1 - - - - - LacI_protein - 1 - - - - - - - - LacI - 1 - - - - - - - - - - YFP_protein_degradation - 1 - - - - YFP_protein - 1 - - - - - - - - - YFP_degradation_interaction - 1 - - - - - YFP_protein - 1 - - - - - - - - - - aTc_TetR_protein_complex_formation - 1 - - - - aTc_TetR_protein - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - aTc - 1 - - - - - - - - - aTc_TetR_protein_complex_formation - 1 - - - - - TetR_protein - 1 - - - - - - - - aTc_TetR_protein - 1 - - - - - - - - aTc - 1 - - - - - - - - - - pTac - 1 - - pTac - 2019-02-20T23:57:58.276Z - - - - - - - - - TetR_protein - 1 - TetR_protein - 2019-02-20T23:57:58.276Z - - - - - ElvJ - 1 - - ElvJ - 2019-02-20T23:57:58.276Z - - - - - - - - - B2 - 1 - - B2 - 2019-02-20T23:57:58.276Z - - - - - - - - - ECK120010876 - 1 - - ECK120010876 - 2019-02-20T23:57:58.276Z - - - - - - - - - Q2 - 1 - - Q2 - 2019-02-20T23:57:58.276Z - - - - - - - - - aTc - 1 - - - - - ECK120015440 - 1 - - ECK120015440 - 2019-02-20T23:57:58.276Z - - - - - - - - - BydvJ - 1 - - BydvJ - 2019-02-20T23:57:58.276Z - - - - - - - - - YFP - 1 - - YFP - 2019-02-20T23:57:58.276Z - - - - - - - - - LacI - 1 - - LacI - 2019-02-20T23:57:58.276Z - - - - - - - - - ECK120010818 - 1 - - ECK120010818 - 2019-02-20T23:57:58.276Z - - - - - - - - - IPTG_LacI_protein - 1 - IPTG_LacI_protein - 2019-02-20T23:57:58.276Z - - - - - aTc_TetR_protein - 1 - aTc_TetR_protein - 2019-02-20T23:57:58.276Z - - - - - YFP_protein - 1 - YFP_protein - 2019-02-20T23:57:58.276Z - - - - - Cello_ecoli_tuTetR - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation2_Range - 1 - 154 - 190 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation_Range - 1 - 1 - 71 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation1_Range - 1 - 72 - 153 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation4_Range - 1 - 815 - 869 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation3_Range - 1 - 191 - 814 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint2 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint - 1 - - - - - - - - - - Cello_ecoli_tuYFP - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation2_Range - 1 - 157 - 193 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation4_Range - 1 - 1080 - 1128 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation3_Range - 1 - 194 - 1079 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation_Range - 1 - 1 - 71 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuYFP_SequenceAnnotation1_Range - 1 - 72 - 156 - - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint2 - 1 - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuYFP_SequenceConstraint - 1 - - - - - - - - - - pTet - 1 - - pTet - 2019-02-20T23:57:58.276Z - - - - - - - - - LacI_protein - 1 - LacI_protein - 2019-02-20T23:57:58.276Z - - - - - TetR - 1 - - TetR - 2019-02-20T23:57:58.276Z - - - - - - - - - IPTG - 1 - - - - - PlmJ - 1 - - PlmJ - 2019-02-20T23:57:58.276Z - - - - - - - - - Cello_ecoli_tuLacI - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation4_Range - 1 - 1250 - 1303 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation3_Range - 1 - 164 - 1249 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation2_Range - 1 - 155 - 163 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation1_Range - 1 - 75 - 154 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation_Range - 1 - 1 - 74 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint2 - 1 - - - - - - - - - - H1 - 1 - - H1 - 2019-02-20T23:57:58.276Z - - - - - - - - - B2_sequence - 1 - - B2_sequence - 2019-02-20T23:57:58.276Z - - - CTATGGACTATGTTTTTCAAAGACGAAAAACTACTAG - - - - - H1_sequence - 1 - - H1_sequence - 2019-02-20T23:57:58.276Z - - - ACCCCCGAG - - - - - Cello_ecoli_tuLacISequence - 1 - - TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCACCTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaaACCCCCGAGatgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaggacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagatagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgccagtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgataaGTCAGTTTCACCTGTTTTACGTAAAAACCCGCTTCGGCGGGTTTTTACTTTTGG - - - - - ECK120010876_sequence - 1 - - ECK120010876_sequence - 2019-02-20T23:57:58.276Z - - - taaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta - - - - - BydvJ_sequence - 1 - - BydvJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaa - - - - - pTac_sequence - 1 - - pTac_sequence - 2019-02-20T23:57:58.276Z - - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATT - - - - - PlmJ_sequence - 1 - - PlmJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAAGTCATAAGTCTGGGCTAAGCCCACTGATGAGTCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAA - - - - - Cello_ecoli_tuYFPSequence - 1 - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATTCTGAAGTCATAAGTCTGGGCTAAGCCCACTGATGAGTCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAACTATGGACTATGTTTTTCAAAGACGAAAAACTACTAGCTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCCtccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca - - - - - LacI_sequence - 1 - - LacI_sequence - 2019-02-20T23:57:58.276Z - - - atgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaggacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagatagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgccagtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgataa - - - - - ECK120015440_sequence - 1 - - ECK120015440_sequence - 2019-02-20T23:57:58.276Z - - - tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca - - - - - Cello_ecoli_tuTetRSequence - 1 - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATTCTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaaGCCATGCCATTGGCTTTTGATAGAGGACAACTACTAGatgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtcctaataaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta - - - - - pTet_sequence - 1 - - pTet_sequence - 2019-02-20T23:57:58.276Z - - - TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCAC - - - - - TetR_sequence - 1 - - TetR_sequence - 2019-02-20T23:57:58.276Z - - - atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtcctaa - - - - - YFP_sequence - 1 - - YFP_sequence - 2019-02-20T23:57:58.276Z - - - CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC - - - - - ElvJ_sequence - 1 - - ElvJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaa - - - - - ECK120010818_sequence - 1 - - ECK120010818_sequence - 2019-02-20T23:57:58.276Z - - - GTCAGTTTCACCTGTTTTACGTAAAAACCCGCTTCGGCGGGTTTTTACTTTTGG - - - - - Q2_sequence - 1 - - Q2_sequence - 2019-02-20T23:57:58.276Z - - - GCCATGCCATTGGCTTTTGATAGAGGACAACTACTAG - - - - - Cello_ecoli_tuYFP_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-17T00:14:44.679-06:00 - - - - Association - 1 - - - - - - - - Cello_ecoli_tuTetR_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-17T00:05:08.085-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2sbol_Activity - 1 - Cello UCF to SBOL conversion - Conversion of the Cello UCF parts and metadata to SBOL 2 documents. - - - 2019-02-20T16:57:58.314-07:00 - - - - association - 1 - - - - - - - - - UCF_file - 1 - - - - - - - - - Cello_ecoli_tuLacI_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-16T23:55:58.519-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2SBOL - 1 - Cello UCF to SBOL - A script to convert Cello UCF parts and metadata to SBOL 2 documents. - - Prashant Vaidyanathan - Chris J. Myers - - - - - - attachment_00009g2fklS69eiQUeolIu - 1 - Eco1C1G1T1-synbiohub.UCF.json - - - - - 3570439 - 57292cc1b8f9be5abbc7a6e6824fdba12f35fb18 - - \ No newline at end of file diff --git a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution2.xml b/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution2.xml deleted file mode 100644 index cefcdee24..000000000 --- a/synthesis/src/test/resources/edu/utah/ece/async/ibiosim/synthesis/outputFiles/tm_solution2.xml +++ /dev/null @@ -1,2685 +0,0 @@ - - - - - LacI_protein_degradation - 1 - - - - LacI_protein - 1 - - - - - - - - - LacI_degradation_interaction - 1 - - - - - LacI_protein - 1 - - - - - - - - - - aTc_TetR_protein_degradation - 1 - - - - aTc_TetR_protein - 1 - - - - - - - - - aTc_TetR_protein_degradation_interaction - 1 - - - - - aTc_TetR_protein - 1 - - - - - - - - - - Cello_ecoli_tuYFP2_module - 1 - - - - Cello_ecoli_tuYFP2_fc - 1 - - - - - - - pTet_mapsTo - 1 - - - - - - - - - YFP_mapsTo - 1 - - - - - - - - - - - pTet - 1 - - - - - - - - - YFP_protein - 1 - - - - - - - - - aTc - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - aTc_TetR_protein - 1 - - - - - - - - - YFP - 1 - - - - - - - - - Cello_ecoli_tuYFP2_module_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP2_module_TetR_protein_degradation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP2_module_aTc_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP2_module_aTc_TetR_protein_degradation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP2_module_YFP_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuYFP2_module_YFP_protein_degradation_sub_YFP_protein_YFP_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP2_module_TetR_protein_pTet_repression_sub - 1 - - - - - Cello_ecoli_tuYFP2_module_TetR_protein_pTet_repression_sub_pTet_pTet - 1 - - - - - - - - - Cello_ecoli_tuYFP2_module_TetR_protein_pTet_repression_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuYFP2_module_aTc_TetR_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuYFP2_module_aTc_TetR_protein_complex_formation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP2_module_aTc_TetR_protein_complex_formation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP2_module_aTc_TetR_protein_complex_formation_sub_aTc_aTc - 1 - - - - - - - - - - - Cello_ecoli_tuYFP2_module_YFP_protein_production_sub - 1 - - - - - Cello_ecoli_tuYFP2_module_YFP_protein_production_sub_YFP_protein_YFP_protein - 1 - - - - - - - - - Cello_ecoli_tuYFP2_module_YFP_protein_production_sub_YFP_YFP - 1 - - - - - - - - - - - YFP_protein_production - 1 - - - - YFP - 1 - - - - - - - - - YFP_protein - 1 - - - - - - - - - YFP_protein_interaction - 1 - - - - - YFP - 1 - - - - - - - - YFP_protein - 1 - - - - - - - - - - TetR_protein_degradation - 1 - - - - TetR_protein - 1 - - - - - - - - - TetR_degradation_interaction - 1 - - - - - TetR_protein - 1 - - - - - - - - - - IPTG_LacI_protein_complex_formation - 1 - - - - IPTG_LacI_protein - 1 - - - - - - - - - IPTG - 1 - - - - - - - - - LacI_protein - 1 - - - - - - - - - IPTG_LacI_protein_complex_formation - 1 - - - - - IPTG_LacI_protein - 1 - - - - - - - - IPTG - 1 - - - - - - - - LacI_protein - 1 - - - - - - - - - - Cello_ecoli_tuLacI_module - 1 - - - - IPTG - 1 - - - - - - - - - LacI - 1 - - - - - - - - - IPTG_LacI_protein - 1 - - - - - - - - - pTet - 1 - - - - - - - - - aTc - 1 - - - - - - - - - Cello_ecoli_tuLacI_fc - 1 - - - - - - - pTet_mapsTo - 1 - - - - - - - - - LacI_mapsTo - 1 - - - - - - - - - - - LacI_protein - 1 - - - - - - - - - aTc_TetR_protein - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_LacI_protein_degradation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_aTc_TetR_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_aTc_TetR_protein_complex_formation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_aTc_TetR_protein_complex_formation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_aTc_TetR_protein_complex_formation_sub_aTc_aTc - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_degradation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_aTc_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_aTc_TetR_protein_degradation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_TetR_protein_degradation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_LacI_protein_production_sub - 1 - - - - - Cello_ecoli_tuLacI_module_LacI_protein_production_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_LacI_protein_production_sub_LacI_LacI - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub - 1 - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub_pTet_pTet - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_TetR_protein_pTet_repression_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuLacI_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - IPTG_LacI_protein_degradation - 1 - - - - IPTG_LacI_protein - 1 - - - - - - - - - IPTG_LacI_protein_degradation_interaction - 1 - - - - - IPTG_LacI_protein - 1 - - - - - - - - - - Cello_ecoli_tuTetR_module - 1 - - - - IPTG - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - IPTG_LacI_protein - 1 - - - - - - - - - aTc_TetR_protein - 1 - - - - - - - - - TetR - 1 - - - - - - - - - pTac - 1 - - - - - - - - - Cello_ecoli_tuTetR_fc - 1 - - - - - - - TetR_mapsTo - 1 - - - - - - - - - pTac_mapsTo - 1 - - - - - - - - - - - LacI_protein - 1 - - - - - - - - - aTc - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_TetR_protein_degradation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_TetR_protein_production_sub - 1 - - - - - Cello_ecoli_tuTetR_module_TetR_protein_production_sub_TetR_TetR - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_TetR_protein_production_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_degradation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_LacI_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_LacI_protein_degradation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_degradation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_degradation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub - 1 - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub_pTac_pTac - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_LacI_protein_pTac_repression_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_IPTG_LacI_protein_IPTG_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_LacI_protein_LacI_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_IPTG_LacI_protein_complex_formation_sub_IPTG_IPTG - 1 - - - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub - 1 - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_aTc_aTc - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_TetR_protein_TetR_protein - 1 - - - - - - - - - Cello_ecoli_tuTetR_module_aTc_TetR_protein_complex_formation_sub_aTc_TetR_protein_aTc_TetR_protein - 1 - - - - - - - - - - - r_s_q_net - 1.0 - - - - FC1_YFP_protein - 1.0 - - - - - - - - - FC3_aTc - 1.0 - - - - - - - - - FC4_IPTG - 1.0 - - - - - - - - - FC0_TetR_protein - 1.0 - - - - - - - - - FC2_LacI_protein - 1.0 - - - - - - - - - M2_Cello_ecoli_tuLacI_module - 1.0 - - - - - MT6_IPTG - 1.0 - - - - - - - - - MT7_LacI_protein - 1.0 - - - - - - - - - MT5_TetR_protein - 1.0 - - - - - - - - - - - M0_Cello_ecoli_tuYFP2_module - 1.0 - - - - - MT0_TetR_protein - 1.0 - - - - - - - - - MT1_YFP_protein - 1.0 - - - - - - - - - - - M1_Cello_ecoli_tuTetR_module - 1.0 - - - - - MT4_TetR_protein - 1.0 - - - - - - - - - MT2_LacI_protein - 1.0 - - - - - - - - - MT3_aTc - 1.0 - - - - - - - - - - - TetR_protein_pTet_repression - 1 - - - - pTet - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - TetR_protein_pTet_repression - 1 - 0.0013 - 4.4 - - - - - pTet_promoter_participation - 1 - - - - - - - - TetR_protein_participation - 1 - - - - - - - - - - TetR_protein_production - 1 - - - - TetR - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - TetR_protein_interaction - 1 - - - - - TetR - 1 - - - - - - - - TetR_protein - 1 - - - - - - - - - - LacI_protein_pTac_repression - 1 - - - - LacI_protein - 1 - - - - - - - - - pTac - 1 - - - - - - - - - LacI_protein_pTac_repression - 1 - 0.0034 - 2.8 - - - - - LacI_protein_participation - 1 - - - - - - - - pTac_promoter_participation - 1 - - - - - - - - - - LacI_protein_production - 1 - - - - LacI - 1 - - - - - - - - - LacI_protein - 1 - - - - - - - - - LacI_protein_interaction - 1 - - - - - LacI_protein - 1 - - - - - - - - LacI - 1 - - - - - - - - - - YFP_protein_degradation - 1 - - - - YFP_protein - 1 - - - - - - - - - YFP_degradation_interaction - 1 - - - - - YFP_protein - 1 - - - - - - - - - - aTc_TetR_protein_complex_formation - 1 - - - - aTc_TetR_protein - 1 - - - - - - - - - TetR_protein - 1 - - - - - - - - - aTc - 1 - - - - - - - - - aTc_TetR_protein_complex_formation - 1 - - - - - TetR_protein - 1 - - - - - - - - aTc_TetR_protein - 1 - - - - - - - - aTc - 1 - - - - - - - - - - pTac - 1 - - pTac - 2019-02-20T23:57:58.276Z - - - - - - - - - TetR_protein - 1 - TetR_protein - 2019-02-20T23:57:58.276Z - - - - - Cello_ecoli_tuYFP2 - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Cello_ecoli_tuYFP2_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuYFP2_SequenceAnnotation4_Range - 1 - 1083 - 1131 - - - - - - - - - - Cello_ecoli_tuYFP2_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuYFP2_SequenceAnnotation1_Range - 1 - 75 - 159 - - - - - - - - - - Cello_ecoli_tuYFP2_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuYFP2_SequenceAnnotation3_Range - 1 - 197 - 1082 - - - - - - - - - - Cello_ecoli_tuYFP2_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuYFP2_SequenceAnnotation2_Range - 1 - 160 - 196 - - - - - - - - - - Cello_ecoli_tuYFP2_SequenceAnnotation - 1 - - - - Cello_ecoli_tuYFP2_SequenceAnnotation_Range - 1 - 1 - 74 - - - - - - - - - - Cello_ecoli_tuYFP2_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuYFP2_SequenceConstraint - 1 - - - - - - - - - Cello_ecoli_tuYFP2_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuYFP2_SequenceConstraint2 - 1 - - - - - - - - - - ElvJ - 1 - - ElvJ - 2019-02-20T23:57:58.276Z - - - - - - - - - B2 - 1 - - B2 - 2019-02-20T23:57:58.276Z - - - - - - - - - ECK120010876 - 1 - - ECK120010876 - 2019-02-20T23:57:58.276Z - - - - - - - - - Q2 - 1 - - Q2 - 2019-02-20T23:57:58.276Z - - - - - - - - - aTc - 1 - - - - - ECK120015440 - 1 - - ECK120015440 - 2019-02-20T23:57:58.276Z - - - - - - - - - BydvJ - 1 - - BydvJ - 2019-02-20T23:57:58.276Z - - - - - - - - - YFP - 1 - - YFP - 2019-02-20T23:57:58.276Z - - - - - - - - - LacI - 1 - - LacI - 2019-02-20T23:57:58.276Z - - - - - - - - - ECK120010818 - 1 - - ECK120010818 - 2019-02-20T23:57:58.276Z - - - - - - - - - IPTG_LacI_protein - 1 - IPTG_LacI_protein - 2019-02-20T23:57:58.276Z - - - - - aTc_TetR_protein - 1 - aTc_TetR_protein - 2019-02-20T23:57:58.276Z - - - - - YFP_protein - 1 - YFP_protein - 2019-02-20T23:57:58.276Z - - - - - Cello_ecoli_tuTetR - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation2_Range - 1 - 154 - 190 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation_Range - 1 - 1 - 71 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation1_Range - 1 - 72 - 153 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation4_Range - 1 - 815 - 869 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuTetR_SequenceAnnotation3_Range - 1 - 191 - 814 - - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint2 - 1 - - - - - - - - - Cello_ecoli_tuTetR_SequenceConstraint - 1 - - - - - - - - - - pTet - 1 - - pTet - 2019-02-20T23:57:58.276Z - - - - - - - - - LacI_protein - 1 - LacI_protein - 2019-02-20T23:57:58.276Z - - - - - TetR - 1 - - TetR - 2019-02-20T23:57:58.276Z - - - - - - - - - IPTG - 1 - - - - - PlmJ - 1 - - PlmJ - 2019-02-20T23:57:58.276Z - - - - - - - - - Cello_ecoli_tuLacI - 1 - - - - - - - - Ter_Component - 1 - - - - - - - - NGA_Component - 1 - - - - - - - - Pro_Component - 1 - - - - - - - - RBS_Component - 1 - - - - - - - - CDS_Component - 1 - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation4 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation4_Range - 1 - 1250 - 1303 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation3 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation3_Range - 1 - 164 - 1249 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation2 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation2_Range - 1 - 155 - 163 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation1 - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation1_Range - 1 - 75 - 154 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceAnnotation - 1 - - - - Cello_ecoli_tuLacI_SequenceAnnotation_Range - 1 - 1 - 74 - - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint1 - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint3 - 1 - - - - - - - - - Cello_ecoli_tuLacI_SequenceConstraint2 - 1 - - - - - - - - - - H1 - 1 - - H1 - 2019-02-20T23:57:58.276Z - - - - - - - - - B2_sequence - 1 - - B2_sequence - 2019-02-20T23:57:58.276Z - - - CTATGGACTATGTTTTTCAAAGACGAAAAACTACTAG - - - - - H1_sequence - 1 - - H1_sequence - 2019-02-20T23:57:58.276Z - - - ACCCCCGAG - - - - - Cello_ecoli_tuLacISequence - 1 - - TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCACCTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaaACCCCCGAGatgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaggacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagatagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgccagtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgataaGTCAGTTTCACCTGTTTTACGTAAAAACCCGCTTCGGCGGGTTTTTACTTTTGG - - - - - ECK120010876_sequence - 1 - - ECK120010876_sequence - 2019-02-20T23:57:58.276Z - - - taaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta - - - - - BydvJ_sequence - 1 - - BydvJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAagGGTGTCTCAAGGTGCGTACCTTGACTGATGAGTCCGAAAGGACGAAACACCcctctacaaataattttgtttaa - - - - - pTac_sequence - 1 - - pTac_sequence - 2019-02-20T23:57:58.276Z - - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATT - - - - - Cello_ecoli_tuYFP2Sequence - 1 - - TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCACCTGAAGTCATAAGTCTGGGCTAAGCCCACTGATGAGTCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAACTATGGACTATGTTTTTCAAAGACGAAAAACTACTAGCTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCCtccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca - - - - - PlmJ_sequence - 1 - - PlmJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAAGTCATAAGTCTGGGCTAAGCCCACTGATGAGTCGCTGAAATGCGACGAAACTTATGACCTCTACAAATAATTTTGTTTAA - - - - - LacI_sequence - 1 - - LacI_sequence - 2019-02-20T23:57:58.276Z - - - atgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaggacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagatagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgccagtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcagtgataa - - - - - ECK120015440_sequence - 1 - - ECK120015440_sequence - 2019-02-20T23:57:58.276Z - - - tccggcaattAAAAAAGCGGCTAACCACGCCGCTTTTTTtacgtctgca - - - - - Cello_ecoli_tuTetRSequence - 1 - - AACGATCGTTGGCTGTGTTGACAATTAATCATCGGCTCGTATAATGTGTGGAATTGTGAGCGCTCACAATTCTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaaGCCATGCCATTGGCTTTTGATAGAGGACAACTACTAGatgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtcctaataaggttgaaAAATAAAAACGGCGCTAAAAAGCGCCGTTTTTTTTgacggtggta - - - - - pTet_sequence - 1 - - pTet_sequence - 2019-02-20T23:57:58.276Z - - - TACTCCACCGTTGGCTTTTTTCCCTATCAGTGATAGAGATTGACATCCCTATCAGTGATAGAGATAATGAGCAC - - - - - TetR_sequence - 1 - - TetR_sequence - 2019-02-20T23:57:58.276Z - - - atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtcctaa - - - - - YFP_sequence - 1 - - YFP_sequence - 2019-02-20T23:57:58.276Z - - - CTGAAGCTGTCACCGGATGTGCTTTCCGGTCTGATGAGTCCGTGAGGACGAAACAGCCTCTACAAATAATTTTGTTTAATACTAGAGAAAGAGGGGAAATACTAGATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACAGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCCTGCAATGCTTCGCCCGCTACCCCGACCACATGAAGCTGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCAATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTTAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAACTCGGTACCAAATTCCAGAAAAGAGGCCTCCCGAAAGGGGGGCCTTTTTTCGTTTTGGTCC - - - - - ElvJ_sequence - 1 - - ElvJ_sequence - 2019-02-20T23:57:58.276Z - - - CTGAagCCCCATAGGGTGGTGTGTACCACCCCTGATGAGTCCAAAAGGACGAAATGGGGcctctacaaataattttgtttaa - - - - - ECK120010818_sequence - 1 - - ECK120010818_sequence - 2019-02-20T23:57:58.276Z - - - GTCAGTTTCACCTGTTTTACGTAAAAACCCGCTTCGGCGGGTTTTTACTTTTGG - - - - - Q2_sequence - 1 - - Q2_sequence - 2019-02-20T23:57:58.276Z - - - GCCATGCCATTGGCTTTTGATAGAGGACAACTACTAG - - - - - Cello_ecoli_tuTetR_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-17T00:05:08.085-06:00 - - - - Association - 1 - - - - - - - - Cello_ecoli_tuYFP2_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-17T00:16:28.962-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2sbol_Activity - 1 - Cello UCF to SBOL conversion - Conversion of the Cello UCF parts and metadata to SBOL 2 documents. - - - 2019-02-20T16:57:58.314-07:00 - - - - association - 1 - - - - - - - - - UCF_file - 1 - - - - - - - - - Cello_ecoli_tuLacI_SBOLDesignerActivity - 1 - Tramy Nguyen - 2019-05-16T23:55:58.519-06:00 - - - - Association - 1 - - - - - - - - CelloUCF2SBOL - 1 - Cello UCF to SBOL - A script to convert Cello UCF parts and metadata to SBOL 2 documents. - - Prashant Vaidyanathan - Chris J. Myers - - - - - - attachment_00009g2fklS69eiQUeolIu - 1 - Eco1C1G1T1-synbiohub.UCF.json - - - - - 3570439 - 57292cc1b8f9be5abbc7a6e6824fdba12f35fb18 - - \ No newline at end of file diff --git a/verification/pom.xml b/verification/pom.xml index 33dbd6693..1c226ea70 100644 --- a/verification/pom.xml +++ b/verification/pom.xml @@ -6,7 +6,7 @@ edu.utah.ece.async iBioSim - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT ../ jar @@ -42,7 +42,7 @@ edu.utah.ece.async iBioSim-dataModels - 3.0.0-SNAPSHOT + 3.1.0-SNAPSHOT