Enzyme cost minimization

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Data and software

Data and model files

Model building for ECM relies on general biochemical information (pathway structures, thermodynamic and kinetic parameters, and omics data) given in table files. These files can be obtained from github .


Enzyme cost minimization has been implemented in MATLAB and relies on table files with biochemical data. MATLAB code and data can be downloaded from github - Documentation can be found here. For a usage example, see the Workflow page.

Python Code

Python code for enzyme cost minimization can be downloaded from github.For a usage example, see the Workflow page or the python program ecoli_ccm_aerobic.py.

NEOS Optimization Server

Another implementation of Enzyme Cost Minimization (by Meike Wortle and Michael Ferris) exists on the NEOS optimization server. Input files can be generated using the MATLAB code mentioned above. The GAMS files for the E. coli model can be used: please unzip the file and upload the individual files to the NEOS website. The fields for files "moietymet", "moietyval", "alpha", and "A" can be left open.