Theoretical bases and a collection of programs for detection of independent pathways from substrates to products and for diassembly of large biochemical networks into smaller subnets.

The software listed below is freely available for academic users and for testing.

In case of commercial use, the users are kindly requested to contact us for agreeing on
a contract of utilization.

Services

METATOOL 5.1 Program for computing the nullspace matrix, elementary modes and other
structural properties of biochemical reaction networks. Octave and Matlab version.
Previous version 5.0
METATOOL 4.x Program for computing the nullspace matrix, elementary modes and other structural
properties of biochemical reaction networks. Stand-alone version.
BlockDiag Program for computing and block-diagonalizing the nullspace matrix to the
stoichiometriy matrix of a chemical reaction network.
OptiMode Program for detecting the elementary mode with the highest molar yield for a specified
substrate - product pair from the output file of METATOOL.
Separator Program for decomposing of large biochemical networks in to smaller ones.
Reducing the number of modes

 A program to calculate elementary modes for the complete variety of external and
internal metabolites and a program to calculate the approximated minimal number of modes
NAD+ metabolism Visualisation of all the elementary modes computed with Metatool 5.1 in the analysis of the
 NAD+ metabolic network. More details about this analysis can be found in
de Figueiredo et al. 2011. Additional information about each elementary mode is displayed
 in the accompanying table.