cobrapy
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opencobra
COBRApy is a package for constraint-based modeling of metabolic networks.
The SBML format allows authors to embed their contact information in the form of a VCard, including given name(s) and surname(s), organization, and e-mail address. Also, there are fields for...
SBML documentation is outdated on https://cobrapy.readthedocs.io/en/stable/io.html. E.g., * remove mentioning of lxml * document python-libsbml correctly * SID not documented correctly (patterns should be given) * Some more words about...
Trying to prevent cobra from prefixing my identifiers when writing SBML, I got this (using the textbook model, model history error is unrelated): `cobra.io.write_sbml_model(model, 'test.xml', f_replace={})` ``` Error encountered trying...
in the SBML model (e_coli_core), if I set the extracellular species as a boundary species (e.g. for kinetic simulation), and then load the model to cobra, even though the exchange...
#### Problem description Here I have a suggestion regarding the JSON/Yaml [scheme](http://cobrapy.readthedocs.io/en/latest/_modules/cobra/io/json.html). Specifically, I suggest to output the fields that have multiple elements (e.g. metChEBIID, rxnECNumbers) as array of string...
#### Problem description It seems like the loopless FVA code is not robust against infeasible solutions when it comes to the Gurobi solver. It does not happen with the GLPK...
For the function cobra.flux_analysis.find_blocked_reactions: If the function is implemented by the scripts below, the number of blocked reactions will be miscalculated, only specific for GLPK solver and not for Gurobi...
#### Problem description I would like to reversibly (within a context) swap co-factors. This unexpectedly results in a `KeyError`. #### Code Sample ```python import cobra from cobra.test import create_test_model config...
@opencobra/cobrapy-core, @gregmedlock we need to make a design choice on the proposed groups and compartments PRs and I'd love to have everyone's input. My apologies that the issues were not...
Tab completion of reaction and metabolite IDs is convenient and widely used in IPython and Jupyter. Falling back on `get_by_id` for IDs that do not match the Python variable-naming rules...
