Minimizing the number of modes

The program EI_EXCHANGE (source code) was developed in the programming language C by Ferdinand Moldenhauer in 2002. It runs on UNIX and WINDOWS platforms. EI is an abbreviation which stands for External and Internal. The program EI_EXCHANGE_1.0.EXE runs on Win32 platforms and expects a data file in ASCII format as used for METATOOL.

Start the program EI_EXCHANGE.EXE from a command line as follows:



EI_EXHANGE_1.0.EXE [path]input.file [path]output.file

If the first option is used, the user is asked for the input and output file names. If the output file has the same extension, the program will be aborted. It is not checked whether there already exists an output file with this name.

After reading the input file the metabolites are systematically set in all possible combinations from internal to external status and vice versa.

The results, i.e. the number of elementary modes and the set of external metabolites are written to an ASCII file. The results of the output file can be sorted using other software, such as Microsoft EXCEL.

The program EI_METROPOLIS_1.0.EXE is a windows-program (WIN32) for the most part developed by Sascha Bulik. The internal algorithms out of METATOOL are contributed to the source code by Ferdinand Moldenhauer. The source code is not intended for UNIX systems. The program generates stochastically a set of external metabolites and calculates the number of elementary modes. Thereafter, the combinatorial optimization problem of minimizing the number of elementary modes is tackled by the Metropolis algorithm. The user has to specify the number of iterations.


T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram, S. Schuster: A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. BioSystems, 2003, 70, 255-270

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