cobrapy
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opencobra
COBRApy is a package for constraint-based modeling of metabolic networks.
### Checklist - [x] I searched the [documentation](https://cobrapy.readthedocs.io). - [x] I looked through [similar issues on GitHub](https://github.com/opencobra/cobrapy/issues). - [x] I looked up "How to do ... in cobrapy" on a...
I'm trying to test the section 8 "Loopless FBA", but I couldn't import plot_helper module. Any changes have been made for this module? Thanks in advance.
#### Problem description If a model annotates reactions as exchanges those are picked up by model.exchanges, however, the external compartment detection does not take this into account. So the model...
Once fixed in optlang, use the better errors in `get_solution` etc to avoid the catch-alls
Please voice your opinion here and state your use-case for the old behavior of setting bounds, i.e., constraining a reaction to a single flux value when setting the lower bound...
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...
The autoapi should be updated: https://cobrapy.readthedocs.io/en/latest/autoapi/cobra/index.html - [ ] to include the latest version of the code - [ ] to enable type annotation (which are possible in the docs...
I am working on a simple implementation of cardinality optimization to find all possible leaks and leak modes of a model, following [this tutorial](https://opencobra.github.io/cobratoolbox/stable/tutorials/tutorialLeakSiphonModes.html). Any suggestion/correction or help testing the...
#### Problem description The JSON format allows annotations as lists of lists, but trying to export such a model as SBML causes an error. This is the case for the...
Hello I am trying to create a cobra model using sample SBML files downloaded from [KEGG converter](http://www.grissom.gr/keggconverter/). The ``io`` method ``read_sbml_model`` is able to generate models from these files, but...
