PoCaB
PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks 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 url{http://pocab.cg.cs.uni-bonn.de/}.
Keywords for this software
References in zbMATH (referenced in 7 articles , 1 standard article )
Showing results 1 to 7 of 7.
Sorted by year (- Errami, Hassan; Eiswirth, Markus; Grigoriev, Dima; Seiler, Werner M.; Sturm, Thomas; Weber, Andreas: Detection of Hopf bifurcations in chemical reaction networks using convex coordinates (2015)
- Heinle, Albert; Levandovskyy, Viktor: The SDEval benchmarking toolkit (2015)
- Samal, Satya Swarup; Grigoriev, Dima; FrÃ¶hlich, Holger; Radulescu, Ovidiu: Analysis of reaction network systems using tropical geometry (2015)
- Samal, Satya Swarup; Grigoriev, Dima; FrÃ¶hlich, Holger; Weber, Andreas; Radulescu, Ovidiu: A geometric method for model reduction of biochemical networks with polynomial rate functions (2015)
- Gerdt, Vladimir P. (ed.); Koepf, Wolfram (ed.); Mayr, Ernst W. (ed.); Vorozhtsov, Evgenii V. (ed.): Computer algebra in scientific computing. 14th international workshop, CASC 2012, Maribor, Slovenia, September 3--6, 2012. Proceedings (2012)
- Grigoriev, Dima; Weber, Andreas: Complexity of solving systems with few independent monomials and applications to mass-action kinetics (2012)
- Samal, Satya Swarup; Errami, Hassan; Weber, Andreas: PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks (2012)