cdanielmachado
commented
3 years ago You're right, thanks for pointing that out. Unfortunately the BIGG database contains multiple formulas for each metabolite. Instead of selecting just one arbitrarily, we opted to include them all, which makes the sbml content invalid. I will try to fix this in the next release.
Regardless of that, this should not affect simulations, and the models should run just fine in tools like reframed, cobrapy, optflux, etc.
smoretti
Hi
I packaged carveme, diamond and gurobi in a container and run the container on a proteome. CarveMe ran quickly and the SBML produced looks promising.
Unfortunately when I sent this SBML (v3) to the SBML validator (http://sbml.org/Facilities/Validator) it returns errors:
A Species object must have the required attributes 'id', 'compartment', 'hasOnlySubstanceUnits', 'boundaryCondition' and 'constant'. In my case boundaryCondition and constant are missing.
The value of attribute 'fbc:chemicalFormula' on the SBML object must be set to a string consisting only of atomic names or user defined compounds and their occurrence. Reference: L3V1 Fbc V2 Section 3.4 Encountered ';' when expecting a capital letter.The chemicalFormula 'HPO4;HO4P' has incorrect syntax.
When more than one formula are available, CarveMe write all of them in fbc:chemicalFormula, even if they are the same formula written in different order.
e.g.
<species id="M_pi_c" name="Phosphate" compartment="C_c" hasOnlySubstanceUnits="true" fbc:chemicalFormula="HPO4;HO4P">