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SBML test suite #105

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sebapersson opened this issue Oct 6, 2023 · 1 comment
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SBML test suite #105

sebapersson opened this issue Oct 6, 2023 · 1 comment

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@sebapersson
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Even though PEtab.jl now has support for models with Catalyst and ModelingToolkit, SBML is the facto standard in system biology. Currently, we use our own SBML importer via SBML.jl, not SBMLToolkit mainly because in order to achieve efficient parameter estimation the importer and parameter estimation software must be able to "talk" to each other (e.g. to handle events, piecewise etc efficiently).

It would be good to test the importer against the test-suite, and produce a list of what is supported and not. For simple cases where we would fail against the test-suite implementing support would be good, while for bigger things like events with delay can implemented upon interest.

Currently the test file can be found at https://github.com/sebapersson/PEtab.jl/blob/Extend_SBML/test/Test_SBML.jl. I am currently done with test 1-962, which also states what is supported and not. But, a goal should be to cover all cases and make list of what is not covered.

This was referenced Oct 11, 2023
sebapersson added a commit that referenced this issue Oct 20, 2023
@sebapersson
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SBML functionality has now been moved to the SBMLImporter.jl package.

This package is tested against the test-suite, and there is a list of which features are supported, and not-supported.

The package imports SBML models for PEtab.jl, meaning that PEtab.jl now has quite extensive SBML support.

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