cobratoolbox
cobratoolbox copied to clipboard
opencobra
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
*Please include a short description of problem here* initCobraToolbox _____ _____ _____ _____ _____ | / ___| / _ \ | _ \ | _ \ / ___ \ |...
*Please include a short description of problem here* Hello. I am Sang Mi Lee from KAIST, South Korea. I have tried to use GIMME which is transcriptomics data integration method....
### Summary `mapExpressionToReactions.m` uses `selectGeneFromGPR` to map expression values to reaction levels. It uses processed gene expression values from `findUsedGenesLevels` and assigns **-1** for genes missing from the model. ###...
*Please include a short description of problem here* hello, I am using a model that is in m7H10 medium: The "model.medium" I is: {'EX_ca2': 1000.0, 'EX_cit': 1.0, 'EX_cl': 1000.0, 'EX_co2':...
I've tried running fastGapFill both on one of my own models and by using runGapFill_Example and in both cases I'm getting an error with the LP solver, first with glpk...
testMgPipe.m: Error using initMgPipe (line 67) Unmatched parameter name '/home/rfleming/work/sbgCloud/code/fork-cobratoolbox/.tmp' must be a string scalar or character vector that can represent a field name. Error in testMgPipe (line 70) init...
*Please include a short description of problem here* Is there a way to use the "readCbMap" function with a ".json" format instead of ".txt" format? **I hereby confirm that I...
*Please include a short description of problem here* Hello, I am running FBA using a mycobacterium tuberculosis model from BIGG (http://bigg.ucsd.edu/models/iEK1008). After run FBA I using the e.coli map of...
* verifyModel reports an error when I run:results = verifyModel(model_original,'simpleCheck',true,'restrictToFields',{'rules'}) error as below: ``` Undefined unary operator '~' for input arguments of type 'string'. Error in checkPresentFields (line 93) if...
*Please include a short description of problem here* Hello, I am using a COBRA model (.mat) from Palsson 2018 (https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-018-0557-y), also it is in the BIGG database in .json format,...