iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
When converting the majority SBML model (see stochastic_model_checking
package sent separately) to prism file, it generated the following
exception:
java.lang.IndexOutOfBoundsException: Index: 2, Size: 2
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
at java.util.ArrayList.get(ArrayList.java:429)
at org.sbml.jsbml.ASTNode.getChild(ASTNode.java:2311)
at
biomodel.util.SBMLutilities.convertMath2PrismProperty(SBMLutilities.java:2454)
at biomodel.parser.BioModel.convertLPN2PRISM(BioModel.java:837)
at analysis.main.Run.execute(Run.java:827)
at analysis.main.AnalysisView.run(AnalysisView.java:1124)
at analysis.main.AnalysisThread.run(AnalysisThread.java:24).
When converting the majority SBML model (see stochastic_model_checking package sent separately) to prism file, it generated the following exception:
java.lang.IndexOutOfBoundsException: Index: 2, Size: 2 at java.util.ArrayList.rangeCheck(ArrayList.java:653) at java.util.ArrayList.get(ArrayList.java:429) at org.sbml.jsbml.ASTNode.getChild(ASTNode.java:2311) at biomodel.util.SBMLutilities.convertMath2PrismProperty(SBMLutilities.java:2454) at biomodel.parser.BioModel.convertLPN2PRISM(BioModel.java:837) at analysis.main.Run.execute(Run.java:827) at analysis.main.AnalysisView.run(AnalysisView.java:1124) at analysis.main.AnalysisThread.run(AnalysisThread.java:24).