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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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Tried to run an Analysis of the GeneticToggle circuit I built following the tutorial, but instead java threw a nullpointerexception. #435

Open buggsley opened 7 years ago

buggsley commented 7 years ago

iBioSim Version 3.0.0-beta

Operating system: Mac OS X

Bug reported by: ilarkin@u.northwestern.edu

Description:

Stack trace: java.lang.NullPointerException at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.math.Evaluator.evaluateExpressionRecursive(Evaluator.java:54) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.math.Evaluator.evaluateOperator(Evaluator.java:745) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.math.Evaluator.evaluateExpressionRecursive(Evaluator.java:72) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.math.Evaluator.evaluateOperator(Evaluator.java:734) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.math.Evaluator.evaluateExpressionRecursive(Evaluator.java:72) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.math.ReactionNode.computePropensity(ReactionNode.java:104) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.HierarchicalSimulation.computeFixedPoint(HierarchicalSimulation.java:897) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.methods.HierarchicalODERKSimulator.initialize(HierarchicalODERKSimulator.java:153) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.methods.HierarchicalODERKSimulator.simulate(HierarchicalODERKSimulator.java:177) at edu.utah.ece.async.ibiosim.analysis.simulation.DynamicSimulation.simulate(DynamicSimulation.java:135) at edu.utah.ece.async.ibiosim.analysis.Run.executeSimulation(Run.java:550) at edu.utah.ece.async.ibiosim.analysis.Run.execute(Run.java:139) at edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisView.run(AnalysisView.java:923) at edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisThread.run(AnalysisThread.java:40)

leandrohw commented 7 years ago

Could you send us the file you are testing this with? For now, you can use the rk45 simulation method.

On Fri, Nov 17, 2017 at 4:12 PM, Buggsley notifications@github.com wrote:

iBioSim Version 3.0.0-beta

Operating system: Mac OS X

Bug reported by: ilarkin@u.northwestern.edu

Description:

Stack trace: java.lang.NullPointerException at edu.utah.ece.async.ibiosim.analysis.simulation. hierarchical.math.Evaluator.evaluateExpressionRecursive(Evaluator.java:54) at edu.utah.ece.async.ibiosim.analysis.simulation. hierarchical.math.Evaluator.evaluateOperator(Evaluator.java:745) at edu.utah.ece.async.ibiosim.analysis.simulation. hierarchical.math.Evaluator.evaluateExpressionRecursive(Evaluator.java:72) at edu.utah.ece.async.ibiosim.analysis.simulation. hierarchical.math.Evaluator.evaluateOperator(Evaluator.java:734) at edu.utah.ece.async.ibiosim.analysis.simulation. hierarchical.math.Evaluator.evaluateExpressionRecursive(Evaluator.java:72) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.math. ReactionNode.computePropensity(ReactionNode.java:104) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical. HierarchicalSimulation.computeFixedPoint(HierarchicalSimulation.java:897) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.methods. HierarchicalODERKSimulator.initialize(HierarchicalODERKSimulator.java:153) at edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.methods. HierarchicalODERKSimulator.simulate(HierarchicalODERKSimulator.java:177) at edu.utah.ece.async.ibiosim.analysis.simulation. DynamicSimulation.simulate(DynamicSimulation.java:135) at edu.utah.ece.async.ibiosim.analysis.Run.executeSimulation(Run.java:550) at edu.utah.ece.async.ibiosim.analysis.Run.execute(Run.java:139) at edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisView. run(AnalysisView.java:923) at edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisThread.run( AnalysisThread.java:40)

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