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Trying to import SBML models containing AlgebraicRules and Events results in `sympy.matrices.common.ShapeError`.
To reproduce: `pytest tests/testSBMLSuite.py::test_sbml_testsuite_case[00662]`, afte…
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Currently only quantitative models are supported for printing reports as a LaTeX document. [SBMLreporter](https://github.com/sbmlteam/SBMLreporter) could be a possible option for implementing such a f…
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### Simulation tool
### Simulation tool
---
id: vcell
version: 7.5.0.27
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.6.0.27/biosimulators.json
specificationsPatc…
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A related question (but we can migrate this to a new Issue if you prefer): your paper mentions adding transport reactions from cytosol to extracellular space when necessary. But the SBML models (wheth…
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A work-in-progress list of things required to support 3d models:
- [x] dune-copasi should already support 3d simulation
- presumably membrane reactions go from a flux across a 1d edge between el…
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The SBML models for plant species provided on the website contain duplicated IDs which makes them fail SBML validation.
This is a redirect from: https://github.com/opencobra/cobrapy/issues/1235 whi…
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Hi, could you,please, clarify what is the current way to import `PEtab` models to `dMod` (in particular SBML files) ? I have tried `PEtab2dmod` library with `libSBML 5.19` but I have a number of issue…
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Example (12119723):
- Native: https://github.com/virtualcell/vcdb/blob/main/published/biomodel/omex/native/biomodel_12119723.omex
- SBML: https://github.com/virtualcell/vcdb/blob/main/published/biom…
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The key idea of memote is that
> Models should, for the benefit of the community and for research gain, live up to certain standards and minimal functionality.
Within the memote manuscript it is…
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When people use legacy models or COBRA matlab models often some confusion arises on
- why there are warnings such as `no fbc package`?
- legacy models do not contain fbc information; this is no…