akaviaLab

I can give some insight into why these might exist biologically. If you have a complex comprised out of 2 alpha unit and 2 beta units to work, the GPR...

I get this with CPlex as well, running MOMA. I don't have much further detail.

rxn.mat is a small matrix distributed in src/reconstruction/rBioNet/rxn.mat and in cobratoolbox/test/verifiedTests/reconstruction/testRBioNet/ which seems to bias the functions of rBioNet. ping @laurentheirendt, @rmtfleming, since I believe you guys wrote rBioNet.

Is this still valid? I'm asking because cobra/sbml.py seems to work well with gz and bz2, both reading and writing

Hi Would you like me to use python modules gzip and bz2 to implement reading/writing of compressed files for the other formats? It would be slightly different from libsbml, which...

Okay - if you can review and hopefully merge #1245, which allows I/O to use Paths, I can build upon that to get all formats to deal with compressed files....

I'd be happy to move it to the testing suite. This really helped me working on MAT import to make sure it is the same as SBML. If I move...

Would you like me to move the compare function to tests? I can do that.

I ran across this problem or a similar one. What about implementing something similar to https://github.com/opencobra/cobratoolbox/blob/develop/src/base/io/utilities/SBML/convertSBMLID.m This is needed for various reasons, but since both read and write SBML call...

@matthiaskoenig - the code does not replace the GIDs when reading old-style SBML files that have the gene association in NOTES field, like Recon 2.2. See example file [exampleModel.xml.gz](https://github.com/opencobra/cobrapy/files/3458773/exampleModel.xml.gz), where...