cobrapy
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opencobra
COBRApy is a package for constraint-based modeling of metabolic networks.
all public objects should be accessible via `import .. from cobra` or predictably one of the few submodules. Go through the package and ensure that everything that should be supported...
So this was brought up in #303 and #389, it might be worth talking about the relative merits / inconvenience of having Reaction, Metabolite, and Gene objects aware of the...
Making a cobrapy 1.0 release is a chance to introduce some breaking API changes, look at the current package design, and organize what belongs in cobrapy and what doesn't. This...
* [ ] Compartment class * [ ] annotations * [ ] groups * [ ] original SBML ID
Hi everyone, I'm trying to reconstruct a first draft of a model with Pathway Tools, using the annotation file Genbank and the genome FASTA curate of NCBI. Then, I export...
So I'll use this issue to kick off the discussion on EFMs and MCSs The two methods I've had the most luck with in calculating EFMs and MCSs are [`efmtool`](http://www.csb.ethz.ch/tools/software/efmtool.html),...
### Checklist - [ ] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. ### Is your feature related to a problem? Please describe it. ## Describe the...
* [x] fix #1279 * [x] description of feature/fix: Add a progress bar to FVA (triggered only during logging.INFO) * [x] tests added/passed * [x] add an entry to the...
### Checklist - [ ] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. ### Is your feature related to a problem? Please describe it. ## Describe the...