Metabolic Adjustment by Differential Expression (MADE)
MADE source code is available under the "Downloads" tab above. Choose "made.tar" under the "Uploaded files" section. The software currently uses either the ILOG CPLEX or Gurobi (via Gurobi Mex) solver. Both are freely available for academic use.
Download and extract the .tar or .zip archive and add the directory (with subfolders) to your MATLAB path. MADE uses metabolic models in the COBRA toolbox format.
MADE uses the CMPI Matlab package to access the MILP solver. CMPI is included in the MADE installation. Before using MADE, call 'cmpi.init()' to initialize the interface. By default, CMPI assumes that ILOG CPLEX is installed and available on the Matlab path. To use the Gurobi solver (via Gurobi MEX), type 'cmpi.set_solver('gurobi')'. For help using CMPI, type 'help cmpi'.
Testing the Installation
The file 'test/test_made.m' tests MADE using a small metabolic model.
Comments or Help
Help for MADE is available by typing 'help made' in Matlab.
Please e-mail Paul Jensen (email@example.com) with any questions or comments.