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MyersResearchGroup / SynBioSuite

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Simulation of hierarchical SBML files #3

Open cjmyers opened 2 years ago

cjmyers commented 2 years ago

A hierarchical SBML file can be broken into multiple SBML files. When an SBML model is selected for simulation, it may have dependencies of other SBML files. The only way to know these dependencies is to parse the SBML file to find them. Another cruder solution would be to send all the SBML files in the current working directory to the simulation server, so they can be included in the simulation as needed.

zachsents commented 2 years ago

Working on a feature to detect dependencies inside SBOL and SBML files. For sending multiple SBML files to iBioSim, would it work to zip them into an OMEX on the client then just send that?

cjmyers commented 2 years ago

Hmm, I think if you provide an OMEX file to the command line, it will expect to find a SED-ML file in the OMEX file. I think a better approach is to send the files in a Zip that gets unpacked at the other end. The command line only needs the name of the top-level file to simulate. It will then find the other files referred to in the local directory.