conda install -c bioconda -c conda-forge cobra.
Hello! I am working with Recon3D and HMR2 .mat files. I am loading them into cobrapy using
cobra.io.load_matlab_model('recon3D.mat'). I can't figure out where the subsystem assignments are stored - any insights?
I have another model (humanGEM) in both .mat and .xml formats. The .xml file has subsystem information stored in "groups", whereas for the .mat file, the groups attribute is empty and I can't find subsystem information. Just wondering if my .mat files are missing the information or if I am loading the .mat files into cobrapy incorrectly...Thank you!
cobra/core/summary/summary.py:206 UserWarning: Setting float_format to anything other than None will cause nan to be present in the output.and really ugly output.
Model.mergewill duplicate reactions that are present in both models which might be problematic if what you really want is a pan-genome model. Micom's
join_modelsuses the union of all reactions (based on IDs) which is a bit different from merge and sets the biomass as the average of all biomass functions. So it depends on your usecase and the particular biological assumptions you make.