FEATURE: add support for general biochemical reactions in logical abstraction

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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FEATURE: add support for general biochemical reactions in logical abstraction #175

Open buggsley opened 7 years ago

buggsley commented 7 years ago

By using reaction splitization idea, support arbitrary reactions when mapping to a logical model.

buggsley commented 7 years ago

I got the following exception when I tried this (will send example in separate message).

Exception in thread "Thread-9" java.lang.NullPointerException at biomodel.parser.BioModel.replaceParams(BioModel.java:966) at biomodel.parser.BioModel.convertToLHPN(BioModel.java:861) at analysis.Run.execute(Run.java:687) at analysis.AnalysisView.run(AnalysisView.java:2207) at analysis.AnalysisThread.run(AnalysisThread.java:24)