cobratoolbox
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opencobra
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
Hi I have ran a microbiome modeling data with 95 samples and about 200 taxons. But it's about 3weeks that is performing FVA with CPLEX 128 (fvatype=1) on 1 sample...
Hi! I've met a bug when I am running testAll. Something seems error in line 149 in testFVA.m, which is assert(verifyCobraFunctionError('fluxVariability', 'outputArgCount', 2, ... 'input', {model, 'o', 90, 'rxnNameList', rxnTest},...
1) % For all reversible reactions, the following equation holds true for the % reverse direction: `vi + c * vrxnC >= u`. I think this should be `vi +...
When using `printRxnFormula`, the function prints wrong genes without replacing and/or operators. Unfortunately, `testPrintRxnFormula.m `bypasses this bug because of the use of `model.grRules` instead of `model.rules`. You can reproduce the...
Hei, I have problems to run gpSampler with 2 threads (or more) on my Mac having 7 cores. My model is E Coli Core model. When I lunch the function...
Pan models
Hi I tried to create pan models in family level, but the result of model test shows me it has leak. what could i do? Is there anyway i test...
When we perform a flux variability analysis only on a set of reactions (and not on the complete model), there might a problem with lines 237, 238 maxSolved = false(size(model.lb));...
*I am trying to use the random sampling method of cobratoolbox to obtain all possible flux distribution for the maximal growth rate condition. I try to fulfill this goal by...
I have faced with this error in mgPipe Error using mergeTwoModels>mergeFields (line 232) Subscript indices must either be real positive integers or logicals what is that for? - [x] Tried...
1. I tried to remove the genes from the model and want to also remove the rxn related from the model if the grrule is empty. I am using the...
