prepHumanModelForftINIT issue when working with MouseGEM

[rsango6]

Hi there,

I am trying to generate ftINIT models with MouseGEM and am following a tutorial on https://sysbiochalmers.github.io/Human-GEM-guide/gem_extraction/

In the preparation step, I am trying to generate a prepData struct with the following code:

prepData = prepHumanModelForftINIT(mouseGEM, false, ...
    '/path/to/Human-GEM/data/metabolicTasks/metabolicTasks_Essential.txt', ...
    '/path/to/Mouse-GEM/model/reactions.tsv');

The error I get is the following:

Step 3: Check tasks (~10 min)
Attempt to grow array along ambiguous dimension.

Error in closeModel (line 50)
        closedModel.b(numel(closedModel.b)+1)=0;

Error in prepINITModel (line 82)
    bModel = closeModel(cModel);

Error in prepHumanModelForftINIT (line 133)
prepDataHumanGEM = prepINITModel(m, taskStruct, spontRxnNames, convertGenes, customRxnsToIgnore, 'e');

I have tried the same thing with HumanGEM, and it successfully passes the third step when it checks metabolic tasks. Any idea why MouseGEM can't do the same? I suspect it is something to do with MetabolicTasks.txt file but not sure exactly what.

Many thanks!

[rsango6]

I was able to solve this:

I had to transform the model into a closed-form, i.e. model = addBoundaryMets(model). I can now proceed through the third step and now can go to other steps in model generation.

[haowang-bioinfo]

very good