Version

Decomptool version 1.0 is available in Corona.

Description

Decomptool can be used to decompose biochemical networks into subnetworks using the algorithm described by Girvan and Newman.

Usage

Before running decomptool in Corona, you must set up the systems biology environment with command:

   use sysbio

A stoichiometry matrix is used to input the biochemical network. Decomptool can read a stoichiometry matrix either from an SBML-file (-s) or from an ASCII matrix file (-m). See the Decomptool manual for detailed description of the ASCII format.

Decompostion of a stoichiometry matrix is preformed with commands:

   decomptool -m ASCII_matrix -o output_tree_file

or

   decomptool -s SBML_file -o output_tree_file

Decomptool output file contains the decomposed network in the Newick tree format.

This tree can be visualized e.g. with drawtree and drawgram programs of the phylip package.

More information

• decomptool manual
• The Newick tree format

References

• Girvan, M. and Newman, M.E.J. (2002) Community structure in social and biological networks. Proc. Natl. Acad. Sci. U.S.A., 99, 7821-7826