How to fix "Model does not contain SBML fbc package information."

Question

I'm trying to simulate some models using SBML package. Model seems to run fine, but I keep getting these warning. "Model does not contain SBML fbc package information. SBML package 'layout' not supported by cobrapy,information is not parsed SBML package 'render' not supported by cobrapy,information is not parsed"

Answer 1

What you see are only warnings that you do not use the SBML fbc package for encoding the constraint-based model information. Most likely all the information like flux bounds and objective function are in your model, but in a legacy format (e.g., COBRA format). A possible way to get your model updated to SBML L3 with fbc is to use the cobrapy import and export, i.e.,

from cobra.io import read_sbml_model, write_sbml_model
model = read_sbml_model(input_path)
write_sbml_model(model, output_path)

The export uses the latest version of fbc.

The warnings about the packages are just an indication that the respective information is not used in cobrapy, i.e., neither layout nor render information are parsed nor used in the context of cobrapy currently.

StackOverflow is not the best forum for cobrapy related questions. Best post issues on https://github.com/opencobra/cobrapy/issues and questions like the above on https://groups.google.com/forum/#!forum/cobra-pie

Disclaimer: I am the author of the cobrapy SBML parser.