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The software provided here is freely accessible and we hope it will be useful. It is provided "as is" and without any warranty whatsoever. If you run into any problems with it, let us know and we will do our best to help. Please keep in mind that (a) all bug-free code is trivial; (b) correcting code can take time; and (c) legacy code may no longer be updatable if the original developers have left the lab. If you use results from our software in a paper, please cite the appropriate reference provided below.

chemical reaction networks | linear framework

chemical reaction networks

reaction-networks.m — a Mathematica package with a custom function MakeCRN. This function takes as input a description of a chemical reaction network and returns as output (1) the deficiency of the network, in the sense of Chemical Reaction Network Theory (CRNT); (2) the polynomial equations arising from mass-action kinetics; and (3) the directed graph on the CRNT "complexes". For more information on CRNT, see Gunawardena, "Chemical Reaction Network Theory for in-silico biologists", preprint, 2003.

linear framework

The linear framework provides a method for time-scale separation in biochemical systems (Gunawardena, PLoS ONE, 2012; Mirzaev, Gunawardena, Bull Math Biol, 2013). It is based on a labelled, directed graph on which a linear (Laplacian) dynamics is defined. If the graph is strongly connected, the steady state of the dynamics is given by the Matrix-Tree Theorem in terms of the rooted, spanning trees of the graph. — a python script which computes the rooted, spanning trees of a graph using Uno's algorithm (Takeaki Uno, "An algorithm for enumerating all directed spanning trees in a directed graph", Springer LNCS 1178, 1996; PDF).

graph-interface.nb — a Mathematica notebook for constructing and manipulating the polynomials that come from the Matrix-Tree Theorem.


  1. From the paper Ahsendorf, Wong, Eils, Gunawardena, submitted, 2014.


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