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PoCaB: A Software Infrastructure to Explore Algebraic Methods for Bio-chemical Reaction Networks

  • Satya Swarup Samal
  • Hassan Errami
  • Andreas Weber
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7442)

Abstract

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/

Keywords

Reaction Network Polynomial System Algebraic Method System Biology Markup Language Stoichiometric Matrix 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Satya Swarup Samal
    • 1
  • Hassan Errami
    • Andreas Weber
      • 2
    1. 1.Bonn-Aachen International Center for Information TechnologyUniversität BonnBonnGermany
    2. 2.Institut für Informatik IIUniversität BonnBonnGermany

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