Frequently asked questions and troubleshooting

Frequently asked questions (FAQs)

Does Human-GEM contain an ATP maintenance reaction?

Yes, MAR03964 is an ATP hydrolysis reaction:

constructEquations(ihuman, 'MAR03964')

ans =

  1×1 cell array

    {'ATP[c] + H2O[c] => ADP[c] + H+[c] + Pi[c]'}

Troubleshooting

Biomass flux is zero

Problem: Running FBA on Human-GEM or a model derived from Human-GEM with a biomass reaction as the objective results in a solution with zero flux, even when all exchange reaction bounds are open.

Solution: Convert the model to "open" format, meaning that it does not contain any "boundary" ("unconstrained") metabolites.

% using RAVEN: use the simplifyModel function
model = simplifyModel(model);

% using COBRA: find and remove all boundary metabolites
[~, boundary_comp_index] = ismember('Boundary', model.compNames);
if isfield(model, 'metComps')
    model = removeMetabolites(model, model.mets(model.metComps == boundary_comp_index));
end

GitHub Discussions

For additional questions and discussions related to Human-GEM, check out the Discussions page within the Human-GEM GitHub repository! Feel free to submit a question there if you cannot find a solution to your problem.