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### Checklist
- [X] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet.
### Problem
Using the same model, implementation of add_loops (addLoopL…
dagl1 updated
4 months ago
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SBO statistics are not calculated correctly.
In the attached screenshot and model example I have either 100% SBO, skipped SBO or errored SBO. I.e. on everything which works I have 100%. How does this…
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When following the Jupyter Notebook availabe on the Escher website, I noticed an error when trying to plot an FBA solution on the E coli core pathway map.
Starting with:
`ecoli = cobra.test.create_t…
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- [ ] With Python
- [ ] With Scipy/Numpy
- [ ] With libsbml
- [ ] with cobrapy
- [ ] with MongoDB
- [ ] With volumes for persistent data storage
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COBRA Models Module folder -> COBRA Models Module Python Files folder -> where could I find iAB_RBC_283.metabolism.json?
I could only find iAB_RBC_283.json in BIGG
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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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So far only `.xml` can be used with refineGEMs. Other fileformats are also being used like `.yml`. It might be of interest to enable other formats or even an automated choice of parser so that a user …
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At the moment, cobrapy changes identifiers when loading a model but reading in the medium does not apply the same transformation leading to mismatches.
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#### Problem description
As noted in https://github.com/SysBioChalmers/yeast-GEM/pull/216, currently there's an inconsistency with how cobratoolbox and cobrapy store gene names in the xml file: cob…
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-TypeError: cannot pickle '_hashlib.HASH' object-
![14B094CE-D203-4017-8D56-559B57C7AD7F](https://github.com/cnapy-org/CNApy/assets/90123540/f4c8f32d-9b5d-4ebd-a93e-d002a139b29b)