cobratoolbox
cobratoolbox copied to clipboard
opencobra
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
solveCobraMILP contains code to remove 'clone1.log' file ([see code]( https://github.com/opencobra/cobratoolbox/blob/2ed83d14eb0e7877856c34ae10f192013b8cdffe/src/base/solvers/solveCobraMILP.m#L316)). Disabling clone logs should be done by passing extra parameters through varargin (concretely, passing an option structure where output.clonelog =...
Should model.rules only be generated on the fly within a function from model.grRules? It seems like people might get dependent on .rules, like they did with .rev as the former...
Hello @tpfau When using writeCbModel and then readCbModel, there are two issues that appear: 1) if no objective function is set (find(model.c) is empty) then model.c is not written. 2)...
Hi, I tried to run fastGapFill with the command "runGapFill_example", and got the following errors: ``` The following problems have been encountered in the model structure inconsistentFields: csense: mets: Size...
Is there a way to calculate the scaled reduced cost instead of the normal reduced cost? **I hereby confirm that I have:** - [X] Tried to solve the issue on...
Hi Is it possible use models other than AGORA models to fulfill metagenomic taxonomies models in MicrobiomeModelingToolbox? If possible, what conditions required for extra models?
https://github.com/opencobra/cobratoolbox/blob/c72a7bd511f79ebc1b6b1e0421544b22b4a9335d/src/reconstruction/rBioNet/neighborRxn2data.m#L44 This is unclear, since it loads up existing data, instead of using the model. Was this perhaps meant to be "rxns"?
isSameCobraModel does not check subSystems. Should this be fixed? One way of fixing it is changing subSystems not to be cells within cell, but I'm not sure why that is...
*Please include a short description of problem here* I tried to execute gapFind.m function and error about SWITCHES came up, I narrowed it down to parseSolverParameters.m function to line s...
https://github.com/opencobra/cobratoolbox/blob/f3fe20df5c977cf0d212e12b1763bd96d15c8760/src/base/solvers/solveCobraQP.m#L601 I appreciate that solveCobraQP checks the max residual in the solution. However, I don't think raising an error is the best solution when a violation occurs. Perhaps we should...
