Additional file 2.

viarray.txt, integrate.cpp, runOPTIMAL.m, runTL.m, integrate.mexw64, OPTIMAL.txt and TLset.txt. “viarray.txt” holds the viability array of the 119 strains (array values of 1 for viable strains and 2 for inviable strains), “integrate.cpp” is the C subroutine for the ODEs and, integrate.mexw64 is the mex file that allows Matlab to use the C subroutine for solving the ODEs. Altogether, these files reproduce the number of hits with the parameter values from the best performing DE run (OPTIMAL.txt from Additional file 2: Table S4, 111 hits) and the initial parameter values (“initial guess”) before the optimization (TLset.txt from Additional file 2: Table S4, with 72 hits). In order to reproduce these results, Matlab files “runOPTIMAL.m” and “runTL.m” need to be executed, respectively.

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Oguz et al. BMC Systems Biology 2013 7:53   doi:10.1186/1752-0509-7-53