(436b) Recent Computational Tools for the Analysis of Complex Biochemical Reaction Networks

Recent
Computational Tools for the Analysis of Complex Biochemical Reaction Networks

Daniel Knight, Haixia Ji, Martin Feinberg

Chemical and Biomolecular Engineering, Ohio State University, Columbus, Ohio

When studying
biological systems, understanding of their dynamical properties is more readily
inferred from knowledge of only the reaction network, as detailed kinetic
information is generally not available with confidence.  There are exemplary complex biochemical reaction
networks with rich behavior (multiple steady states, oscillatory behavior,
etc.), while others have relatively dull, stable dynamics.  Recent theoretical developments^{1, 2}
allow for powerful statements to be made about the dynamics of even very
complex networks, provided the kinetics falls within a very general and natural
class.  In particular, it is possible to
distinguish in a precise way between networks that might provide the basis for
a bistable switch, and networks ? even very intricate ones ? that cannot.  These recent theoretical developments have
been incorporated into a freely available computer program, Chemical Reaction
Network Toolbox (CRNT)³.  The
theory will be discussed, and examples of its implementation via the Toolbox
will be given.

1.  G. Shinar and M. Feinberg, Concordant Chemical Reaction Networks,
2011, available at www.arXiv.org/pdf/1109.2923v1.pdf.

2.  G. Shinar and M. Feinberg, Concordant Chemical Reaction Networks and
the Species-Reaction Graph, 2012, available at www.arXiv.org/pdf/1203.6560v3.pdf.

3.  H. Ji, P. Ellison, D. Knight, and M. Feinberg, The chemical reaction network toolbox, version 2.1, 2011, available at
http://www.chbmeng.ohiostate.edu/ feinberg/crntwin/.