Extreme Pathway Analysis

Extreme Pathway Analysis

An ExPA program (2001)

  • An example input file (Red Blood Cell metabolism) for ExPA program

A new ExPA program (02/16/05)

  • Accepted as an Application Note in Bioinformatics
  • Zip file includes: Program, help files, and input files

A new Linux ExPA program (02/16/05) -Linux Version

  • Tar file includes: Source code, help files, and input files

A new Mac ExPA program (1/25/05) -Mac OSX Version

  • Courtesy of Dr. Ranjan Srivastava (srivasta@engr.uconn.edu),
    Assistant Professor, University of Connecticut

  • Zip file includes: Program, help files, and input files

  • To use, simply launch a terminal window and type "macexpa.out (input file)" at the prompt. Before using the first time, the program might need to be converted into an executable by typing "chmod u+x macexpa.out" at the prompt. The program will generate the output in the "Paths.txt" file, as with the original code.

A Mathematica notebook for calculating ExPas (04/06/06) A simple Mathematica notebook for calculating extreme pathways. 3 examples are included. Users only have to evaluate two cells to calculate extreme pathways! A brief documentation is also available from here.

X3 C++ Extreme Pathway program for large scale networks. (2/23/07)

Related Publications

Yeung, M., Thiele, I., and Palsson, B.Ø., Estimation of the number of extreme pathways for metabolic networks., BMC Bioinformatics, 8(1): 363 (2007).

Bell, S.L. and Palsson, B.Ø., "A Program for Calculating Extreme Pathways in Biochemical Reaction Networks", Bioinformatics, in press (2004).

Papin, J.A., Stelling, J., Price, N.D., Klamt, S., Schuster, S., and Palsson,B.Ø., "Comparison of Network-Based Pathway Analysis Methods", Trends in Biotechnology, 22(8): 400-4055 (2004).

Papin, JA, Price, ND, and Palsson, B.Ø., "Extreme pathway lengths and reaction participation in genome-scale metabolic networks", Genome Res., 12(12): 1889-1900 (2002).

Wiback, SJ and Palsson, B.Ø., "Extreme pathway analysis of human red blood cell metabolism", Biophys. J., 83(2): 808-818 (2002).

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9500 Gilman Drive La Jolla, CA 92093-0412

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