For convenience, we provide the SBMLToolbox 4.1.0, and glpk_mex in external/toolboxes for Mac OS X 10.6 or later (64-bit), GNU/Linux Ubuntu 10.0 (64-bit), and Microsoft Windows 7 (64-bit). If you do not wish to use these items please delete the directories. If you require these external libraries for other architectures please ask google or visit their respective websites. To read / write SBML files you must install libSBML 5.5.0 from here: http://sourceforge.net/projects/sbml/files/libsbml/ From MATLAB, run initCobraToolbox NOTE: If you do not have gurobi_mex and tomlab installed on your machine, you will get some warnings and some errors. The COBRA Toolbox will try to use glpk if it cannot find gurobi for LP / MILP. To solve any NLP problems you need tomlab_snopt. After running initCobraToolbox, run testAll to see what functions will work with your current configuration. Note, it is likely that one or more functions will not work unless you have tomlab with snopt installed.