OpenSourceBrain / SBMLShowcase

OSB showcase of interactions between SBML and NeuroML
http://www.opensourcebrain.org/projects/sbmlshowcase
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Check biosimulators compatibility tables #61

Closed stellaprins closed 1 month ago

stellaprins commented 1 month ago
stellaprins commented 1 month ago

I've updated the engine dict, making the changes we discussed today for Brian2 and NetPyNE.

Engine information was taken from the biosimulators docs (here). E.g. the Brian2 page lists the following compatibility:

COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in NeuroML / LEMS format).

stellaprins commented 1 month ago

I realised I put a placeholder for the Smoldyn compatible formats because I could not find them. From the documentation here, I gather that any model model format is Smoldyn compatible when it is packaged as an omex file with a valid SED-ML file? @pgleeson @sanjayankur31, do you know whether this is correct?

pgleeson commented 1 month ago

@stellaprins I get the impression that the only real format Smoldyn supports is its own, so an omex file with a sed-ml pointing to a smoldyn model is fine for it, but anything else it will fail. I think Smoldyn can export to sbml, but that's not relevant in this scenario.

stellaprins commented 1 month ago

Thanks @pgleeson! Will update the engines dict.