cobratoolbox
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opencobra
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
people often forget to install curl and then installation does not proceed correctly. better to remove it.
Dear Cobra-Team I noticed that cobra 0.26.3 depends on numpy=1.13. With more and more packages moving to numpy>=1.24 I suggest updating this dependency. The incompatible right now is, that np.float64...
Hello, When i tried to run "FVAOptForce" function of cobratoolbox with gurobi v9.5.2 in Matlab R2022b, an Error generated as below. Code) .. constrWT = struct('rxnList', {{'Biomass'}}, 'rxnValues', floor(growthRate.f), 'rxnBoundType',...
defaultSboTerm is not defined in line 496 of writeSBML function. It should be set as defaultSboTerm = 176 **I hereby confirm that I have:** - [ ] Tried to solve...
Is there any way to create compartment data for a metabolic model as shown here  **I hereby confirm that I have:** - [X ] Tried to solve the issue...
sphinxcontrib-matlabdomain 0.19.0 pre-release Hi I'm the main author and maintainer of the `sphinxcontrib-matlabdomain` Python package. I just finished a major update of the extension and added a new configuration option:...
Hello, I tried to run 'GDLS' function with a Model from article. In the previous version of GDLS, the KOs list was output, but in the current version, nothing is...
Hi, I am using a genome-scale model and it's format is ".omex". Does anyone know how can I properly import the model in Matlab cobratoolbox? I tried opening the file...
Hi there, I am trying to figure out the Pareto optimality script of yours. I was wondering if there is any chance that in [line 74](https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/pairwiseInteractionModeling/computeParetoOptimality.m#L74) `rxn2` should be replaced...
*Please include a short description of problem here* https://github.com/opencobra/cobratoolbox/blob/37c922c422a19d731da66e81059ec0989db39418/src/base/io/utilities/SBML/getBioQualifiers.m lists several qualifiers in a single list, but some of them come from different lists; see: https://web.archive.org/web/20211204231945/http://co.mbine.org/specifications/qualifiers In particular, 'isDerivedFrom', 'isInstanceOf',...
