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Repeat exercise from issue #57 for a more (later) BioModels (ideally those that have SBML files that were generated by the authors).
Picked with help of [BioModels results table](https://github.co…
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Filed in [this ](https://github.com/NeuroML/pyNeuroML/issues/435)pyNeuroML issue and fixed in [this ](https://github.com/NeuroML/pyNeuroML/pull/436)PR.
- [ ] use pyNeuroML confirm_file_type for fi…
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Every biomodels that uses steady state uses the KISAO term 282 ('KINSOL'), and the checker returns this error:
NotImplementedError: Algorithm substitution for "KINSOL" (http://www.biomodels.net/ki…
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The guidance document states (4.3.1) that there is a description property for a simulation in the sedml.
- [ ] update Writer Node by adding description to sedml
- [ ] update simulation configurato…
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Running the bio simulator, just freezes whenever the `StandardOutputErrorCapturer` is used. When I run without log file, it works, however no output is produced. so
```python
config = bio…
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Currently the SEDML xpath expressions are resolved via heuristic from xpath string without using the xml of the model. This should be changed to use xpath from xml library with model xml.
This curre…
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In project ```4a6``` the sedml file loads the model on line 22 as follows
```xml
```
However, the source should point to the ```model.cellml``` file instead.
```xml
…
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= Description =
- Provide the API for adding or removing parameters in SBML models through the Change mechanism in SED-ML.
= Context =
- Parameters are used in reaction nodes in the SBML language; it…
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= Description =
- Provide the API for adding or removing reactions in SBML models through the Change mechanism in SED-ML.
= Context =
- Biochemical reactions are central to the SBML language; it shou…
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= Description =
- Provide the API for adding or removing compartments in SBML models through the Change mechanism in SED-ML.
= Context =
- Compartments are an important element of the SBML language, …