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MyersResearchGroup / iBioSim

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.
http://www.async.ece.utah.edu/ibiosim
Apache License 2.0
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Java Array index Error in SSA-Direct Reaction-based Abstraction #609

Open buggsley opened 4 years ago

buggsley commented 4 years ago

iBioSim Version 3.0.0

Operating system: Windows 10

Bug reported by: micotner9@gmail.com

Description: When trying to preform a reaction-based abstraction on my model using the SSA-Direct (Dynamic) simulator, iBioSim immediately throws an error: "java.lang.IndexOutOfBoundsException: Index: 0, Size: 0" The model is BIOMD0000000565 from the EMBL-EBI BioModels database. All simulation options were left as default except: Abstraction was set to Reaction-based, analysis type was set to Monte Carlo, and Possible Simulators/Analyzers was set to SSA-Direct (Dynamic).

Stack trace: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(Unknown Source) at java.util.ArrayList.get(Unknown Source) at org.sbml.jsbml.ASTNode.getChild(ASTNode.java:2498) at org.sbml.jsbml.ASTNode.getLeftChild(ASTNode.java:2620) at edu.utah.ece.async.ibiosim.analysis.simulation.flattened.Simulator.setupSingleReaction(Simulator.java:6299) at edu.utah.ece.async.ibiosim.analysis.simulation.flattened.Simulator.setupReactions(Simulator.java:6548) at edu.utah.ece.async.ibiosim.analysis.simulation.flattened.SimulatorSSADirect.initialize(SimulatorSSADirect.java:270) at edu.utah.ece.async.ibiosim.analysis.simulation.flattened.SimulatorSSADirect.(SimulatorSSADirect.java:51) at edu.utah.ece.async.ibiosim.analysis.simulation.DynamicSimulation.simulate(DynamicSimulation.java:98) at edu.utah.ece.async.ibiosim.analysis.Run.executeSimulation(Run.java:466) at edu.utah.ece.async.ibiosim.analysis.Run.execute(Run.java:148) at edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisView.run(AnalysisView.java:907) at edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisThread.run(AnalysisThread.java:43)

michaelcotner commented 4 years ago

The model that I used was downloaded from https://www.ebi.ac.uk/biomodels-main/BIOMD0000000565

zgzn commented 4 years ago

@cjmyers This is the error for the multi-compartment SBML model we emailed you before. Can you give us pointers on how to fix it? Thanks.

cjmyers commented 4 years ago

Please try this again using the rkf45 ODE simulation method (the method you used is not very stable). If you don't see this one, please make sure you have reb2sac installed. This is also a stiff model, so I set a time limit of 1.0 seconds. It take a long time to simulate, so it likely has a very fast time constants. Do not use abstraction on this model as it will not help.