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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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CHANGE: use SED-ML for all analysisView properties #132

Open buggsley opened 8 years ago

buggsley commented 8 years ago

Create SED-ML annotations for any analysisView properties not already supported in our SED-ML file.

cjmyers commented 6 years ago

The missing ones are: 1) Report Concentrations 2) Do Not Generate Runs (null.printer) 3) Append Simulation Runs (start.index) 4) Generate Statistics 5) All the advanced options

cjmyers commented 6 years ago

Append simulation runs results in number of runs stored as number of runs plus start index.

cjmyers commented 6 years ago

All advanced options are now stored in SED-ML except the pre-loop-post abstraction choices. For now, let's leave these in the properties file since not relevant to anyone but reb2sac. Default are fine when we get a new SED-ML file.

1, 2, 4 above are also not in SED-ML. They largely will affect the data generators. Let's delay this to 3.1.