ERNEST: a toolbox for chemical reaction network theory

Bioinformatics, 25(21), pp. 2853-2854, 2009

Nicola Soranzo, Claudio Altafini
SISSA, Trieste, Italy

ERNEST Reaction Network Equilibria Study Toolbox is a MATLAB package which, by checking various different criteria on the structure of a chemical reaction network, can exclude the multistationarity of the corresponding reaction system.

Paper

• Paper (preprint) of the article

Software

ERNEST 1.4 was released on October 27th, 2009.

Changes in this release:

• Corrected a bug in @umultigraph/walk2graph and @umultigraph/spanning_forest where the call to @umultigraph/umultigraph function was not respecting the stricter type checking introduced in ERNEST 1.2 . Thanks to prof. Gregory D. Smith for the bug report
• Corrected a bug in the creation of a directed multigraph from vertex and edge sets
• Added a display function for directed multigraphs
• Added graph2matrix function for directed and undirected multigraphs
• Added a new script examples/example6.m with examples from Angeli, De Leenheer, Sontag - J. Math. Biol.
• Added an output file for each example

Download: ERNEST 1.4 (.tar.gz)
This software is available under the GNU GPL license version 2 or later.

Useful links

• Mathworks MATLAB
• Mathworks Optimization Toolbox
• Systems Biology Markup Language (SBML)
• libSBML