cobrapy
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opencobra
COBRApy is a package for constraint-based modeling of metabolic networks.
## Problem Description If we read a SBML model, from the corresponding XML file and write it back, then, if the annotation field of some component had more than one...
Hi all, @draeger, @matthiaskoenig, @Midnighter, @cdiener, and other members of COBRApy. I am opening a new thread for discussing about the implementation of Group package in COBRApy as I could...
#### Problem description As noted in https://github.com/SysBioChalmers/yeast-GEM/pull/216, currently there's an inconsistency with how cobratoolbox and cobrapy store gene names in the xml file: cobratoolbox uses the `fbc:label` field, whereas cobrapy...
Trying to convert models with -inf/inf bounds to json fails with ``` Traceback (most recent call last): File "/home/mkoenig/git/pancreas_model/pypancreas/pancreas/model_factory.py", line 51, in cobra.io.save_json_model(model, MODEL_JSON) File "/home/mkoenig/envs/pancreas/lib/python3.6/site-packages/cobra/io/json.py", line 110, in save_json_model...
#### Problem description I'm trying to use the function `cobra.io.sbml.read_sbml_model` to load a sbml model that I generated using function `cobra.io.write_sbml_model`. The model passed the online SBML validator checking, though...
So I though i would share an extensions to slim_optimize that has proven helpful for what i suspect is a fairly common task when performing FBA. I don't know if...
In the current version of cobrapy, the default `processes` attribute of the `Configuration` object is often set to the output of `multiprocessing.cpu_count` function. This behavior results in setting the `processes`...
When I run the example from your loopless FBA documentation, I get the objective value 0 (which is also displayed in the rich output), while the flux of the biomass...
#### Problem description When going through an I/O cycle with a model that has subsystems stored as groups, the members of each group in the sbml file get scrambled on...
#### Problem description Hello guys, I was playing around when cobra refused to export a model to SBML with a TypeError: `TypeError: in method 'Reaction_setReversible', argument 2 of type 'bool'`....
