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- Split SBMLShowcase/.github/workflows/non-omv.yml in two to separate docker / biosimulators related workflows (see below) to differentiate between biosimulators issues and issues with our code.
``…
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### Checklist
- [X] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet.
### Problem
I been trying to work on some metagenome analysis with cobr…
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I tried to use the code to build model:
Combine_PURE=ChemicalReactionNetwork(species = flatten([CRN_TX.species, CRN_TL.species, gfp_species,degraded_species]), reactions = flatten([CRN_TX.reactions, …
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As mention in [this comment](https://github.com/MetabolicAtlas/standard-GEM/issues/9#issuecomment-690221845), the SBML file should contain taxonomy name, taxonomy ID, and reference genome.
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This feature has been requested and would be useful. It's on the google groups thread: https://groups.google.com/forum/#!topic/kroneckerbio-users/__aVJ6GjF9c. We used to have is when we still used sym…
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Running stuff through valgrind, I came across the error:
```
==4973== Conditional jump or move depends on uninitialised value(s)
==4973== at 0xD75631: libsbml::Transformation2D::readAttributes…
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Hi folks,
I love BioTapestry, and wanted to know if there was a way to export the coordinates from your layouts into other graph-rendering software, such as Cytoscape? I see that you can export to…
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Here's links to all the biomodels that currently fail when running PySCeS:
[pysces_failures.csv](https://github.com/biosimulators/Biosimulators_PySCeS/files/13193249/pysces_failures.csv)
(Many o…
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At some point it would be convenient to replace the current SBML-sympification by https://github.com/dweindl/sbmlmath/.
This gives us better control over the whole process and can replace the awkwar…
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It would be great to have the feature of a PEtabSDEProblem, where the model is not a ODe but a SDE.
Maybe for a start, supporting the conversion of a SBML model to an `SDEProblem` would be a good st…