Enzyme cost minimization
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.
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 NEOS 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.