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PNNL-CompBio / CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia
Apache License 2.0
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Ensure universal stoichiometric matrix can run in cobra #22

Closed djinnome closed 1 year ago

mcnaughtonadm commented 1 year ago

Found CobraPy compliant Universal BIGG Model here. This provides access to full Universal model with 15638 Reactions and 28301 metabolites. Able to generate necessary stoichiometric matrix and optimization through CobraPy.

mcnaughtonadm commented 1 year ago

Small Update: To use Gurobi with this universal model, you must first rename or remove the "St" bigg reaction. This just so happens to be a keyword in the LP files that gurobi constructs from the model and it will not process the file. This problem isn't present when using other solvers (it may happen using CPLEX), so just be aware.

djinnome commented 1 year ago

Wow, that is quite a bug! Thanks for figuring out a workaround