FBA solutions are different between Mackinac and Cobra

mmundy42 / mackinac

Mackinac: A bridge between ModelSEED and COBRApy

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FBA solutions are different between Mackinac and Cobra #4

Open liaochen1988 opened 5 years ago

liaochen1988 commented 5 years ago

I generated a metabolic reconstruction using Mackinac and found that the objective values obtained between Mackinac (mackinac.optimize_modelseed_model) and Cobra (model.optimize()) are different. The former gives 1.66 while the latter gives 38.65. Does anyone know what causes this inconsistency? Thanks very much.

mmundy42 commented 5 years ago

Most likely it is because there are different solvers being used by the two systems when optimizing a model. I think ModelSEED is still using SCIP as the solver. You can choose what solver to use with Cobra with GLPK, Gurobi, and CPLEX being the most common.