Create a Tissue-specific GIMME-based Model with the Cobra Toolbox

[fatima niki]

Hi

In this script function getExpD is unknown for MATLAB so ExpressionData too could anyone help me 

load('Recon2.mat');

ExpressionData = getExpD('EID.txt','AP.txt');

[ARPE19_GIMME,Rxns] = createTissueSpecificRec(Recon2_2,ExpressionData,1,1,[],'GIMME',options,1);

writeCbModel(ARPE19_GIMME,'sbml','ARPE19_GIMME_Model');

[Trust Odia]

Fatima,
             extract this file to your working directory and rerun your command.

[Trust Odia]

my challenge is below: i need help on this. i have been battling with this for months

>> [ARPE19_Shlomi,Rxns] = createTissueSpecificModel(Recon2_2,ExpressionData,1,1,[],'Shlomi',options,1);
Error using cell/setdiff>cellsetdiffR2012a (line 292)
Input A of class cell and input B of class double must be cell arrays of
strings, unless one is a string.

Error in cell/setdiff (line 84)
    [varargout{1:nlhs}] = cellsetdiffR2012a(varargin{:});

Error in createTissueSpecificModel>mapProbes (line 471)
unknown = setdiff(unknown,rxnExpressed);

Error in createTissueSpecificModel (line 144)
[ExpressedRxns,UnExpressedRxns,unknown] =
mapProbes(parsedGPR,corrRxn,locus,genePresence,match_strings);

On Friday, May 6, 2016 at 10:34:30 AM UTC+1, fatima niki wrote:

[Xu Zixiang]

Dear All

  I was using the GDLS function in COBRAtoolbox, but the return maxKO is always 1, not the set 8.

       load('ecoli_1260.mat');

       model = changeRxnBounds(model,{'EX_o2(e)','EX_glc(e)'},[0 -10],'l');

       [gdlsSolution] = GDLS(model, 'EX_succ(e)', 'minGrowth', 0.05, 'maxKO', 8, 'koType', 'genes');

   How to get a defined number of KOs ?

 

2016-06-09

---

Xu

[Trust Odia]

Hello,

    can u create ExpressionData used by createTissueSpecificModel function??? which function can I use to do this???

[fatima niki]

Hi thanks for your share i am working with Recon 1 and now I dont know how to calculate objective function and do FBA for my model do you help me ?