[ANN] SBMLToolkit importer of biomodels

What is SBMLToolkit?
We recently released SBMLToolkit.jl, an importer of dynamic biological models specified in the Systems Biology Markup Language (SBML) to the SciML ecosystem. For constraint-based modeling please refer to COBREXA.jl.

Why did we develop SBMLToolkit?
Every dynamic model that people publish should be able to automatically translate to this solver ecosystem to help it scale and parallelize. This will give the biological community the mechanism to reach a new scale of systems biology, whole-cell models and microbiome ecosystems where the modeling process takes only days and the simulation is plausible. SBMLToolkit is the component that makes this missing connection.

What is SBML?
SBML is a software-agnostic community standard for exchanging and storing biological models. There are currently several hundred, manually curated dynamical models in the BioModels database. SBML is based on XML and has a widespread software support that now also includes the Julia programming language. SBML describes models in a chemical-reaction centric way. While it is possible to specify mathematical rather than chemical equations, SBMLToolkit currently only supports SBML models that can be converted to ModelingToolkit.ReactionSystems. We plan to extend our support to further SBML elements. Please get in touch if you want to contribute.

The SciML ecosystem for creating models of biological systems

Main developers
@paulflang , @anandj and @MirekKratochvil . Big thanks also to @laurentheirendt and @ChrisRackauckas for their advice!


Don’t leave out ReactionNetworkImporters for the BioNetGen format, though it is comparatively less widely used than the other two.

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Thanks. I just updated the figure.


Awesome figure BTW.

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BTW, could you open a PR to MTK adding downstream tests on SBMLToolkit and CellMLToolkit? Now that we are counting this area of the ecosystem as released, I want to make sure all of the bots are setup so that it has full stability.

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What kind of downstream tests are you thinking of? I just had a look at the MTK/test/ directory. There’s a lot in there, but did not find existing tests for other upstream tools that go in that direction.