cobrapy
cobrapy copied to clipboard
opencobra
COBRApy is a package for constraint-based modeling of metabolic networks.
Hey @opencobra/cobrapy-core, I'd like to store some meta information about the SBML that was parsed: 1. level 2. version 3. packages used (fbc, annotation, groups) The big question is where...
#### Problem description The system of confidence scores which has been proposed in the past is simple albeit overly-simplified and difficult-to-verify. Using an evidence ontology coupled directly with cross-references to...
This is a far reaching change that I would be rather conservative about. I'm happy to probe the community but maybe the ability to change the global configuration to include...
There have been discussions in #805 and #811 about handling infinity values on bounds and thus basically introducing free or partially free reactions. Overall the consensus seems to be that...
@HAHerrmann a new issue seemed more fitting. > I have been using the ACHR sampler using cobra both in Matlab and Python. In Python when plotting the flux distributions it...
#### Problem description To future-proof cobrapy it migh make sense to offer compartments not just as a dictionary but as objects like all the other model components. While adding little...
#### Problem description Tried to debug it for weeks now, but never found a fix. So reporting it here for now... The following code will slowly consume all memory on...
I don't know if this should be posted here since I already solved my issue, but I think it could be added to the documentation to prevent other people having...
Nowadays, I am working on sampling with recon2. Since sampling is an expensive operation and recon2 model is a pretty big model, I am benchmarking and looking for any possible...
Hi there! Thanks for all the excellent work on cobrapy! Is there any reference/wiki page/comparison table that shows which functionality/methods on the Matlab version are available (or not) on the...
