PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks. (English) Zbl 1373.92002

Gerdt, Vladimir P. (ed.) et al., Computer algebra in scientific computing. 14th international workshop, CASC 2012, Maribor, Slovenia, September 3–6, 2012. Proceedings. Berlin: Springer (ISBN 978-3-642-32972-2/pbk). Lecture Notes in Computer Science 7442, 294-307 (2012).
Summary: Given a bio-chemical reaction network, we discuss the different algebraic entities e.g. stoichiometric matrix, polynomial system, deficiency and flux cones which are prerequisite for the application of various algebraic methods to qualitatively analyse them. We compute these entities on the examples obtained from two publicly available bio-databases called Biomodels and KEGG. The computations involve the use of computer algebra tools (e.g. polco, polymake). The results consisting of mostly matrices are arranged in form of a derived database called PoCaB (Platform of Chemical and Biological data). We also present a visualization program to visualize the extreme currents of the flux cone. We hope this will aid in the development of methods relevant for computational systems biology involving computer algebra. The database is publicly available at http://pocab.cg.cs.uni-bonn.de/.
For the entire collection see [Zbl 1246.68035].


92-04 Software, source code, etc. for problems pertaining to biology
92C40 Biochemistry, molecular biology
92E20 Classical flows, reactions, etc. in chemistry
92-08 Computational methods for problems pertaining to biology
Full Text: DOI