Problem with loading model

[Ya Meng]

Hi all, I'm tyring to use cobrapy to load a model, but the numbers of metabolites and reactions changed. The following picture shows the results. 

However the paper I'm reading indicates that"The initial C. albicans CoReCo model (BioModels ID 1604280052) comprised 2770 metabolites and 3298 reactions, of which 3150 were network and 148 transport reactions". How can I get the right results?

[Ya Meng]

the results I got were 2946 metabolites and 6193 reactions, but it actually contains 2770 metabolites and 3298 reactions.

[Matthias König]

One thing which changes the number of metabolites and reactions is how the boundary conditions are handled in the model.

If no boundary reactions are defined the boundary species are changed to boundary reactions. This could explain why you see a different number of of reactions and species. Otherwise what you see in cobrapy is what is in the SBML file. Often the numbers reported in the publications differ from the actual numbers in the SBML files.

Best Matthias

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