when I use the iMAT option to create a specific model with createTissueSpecificModel, the models I receive are not cropped down, but are the same size, as before.
I tried this as well with the test-dataset provided with the COBRA installment, but also receive a model of the same size as the input model (here recon1).
This phenomena does not occur with the GIMME option, but I would be glad if I could use iMAT, as I don't want to be relying on an objective function (which is required by GIMME).
I am using COBRA 2.0.3 with Gurobi v4.61and gurobi mex v1.61 on 64 bit Linux.
We have come across this problem before. The problem has to do with the model used for the test, not the algorithm or expression data. I can send you a working Recon1 for iMAT if you like if you email me directly at aabordba_AT_ucsd_edu. This should fix the problem.