SNA--a toolbox for the stoichiometric analysis of metabolic networks

BMC Bioinformatics
Robert Urbanczik

Abstract

Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem. SNA is a interactive, high performance toolbox for analysing the possible steady state behaviour of metabolic networks by computing the generating and elementary vectors of their flux and conversions cones. It also supports analysing the steady states by linear programming. The toolbox is implemented mainly in Mathematica and returns numerically exact results. It is available under an open source license from: http://bioinformatics.org/project/?group_id=546. Thanks to its performance and modular design, SNA is demonstrably useful in analysing genome scale metabolic networks. Further, the integration into Mathematica provides a very flexible environment for the subsequent analysis and interpretation of the results.

References

May 1, 1999·Bioinformatics·T PfeifferS Schuster
Nov 15, 2002·Nature·Jörg StellingErnst Dieter Gilles
Oct 21, 2004·Nature Reviews. Microbiology·Nathan D PriceBernhard Ø Palsson
Sep 29, 2005·Bioinformatics·R Urbanczik, C Wagner
Dec 13, 2005·The FEBS Journal·Jörg W Stucki, Robert Urbanczik

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Citations

Nov 19, 2008·Applied Microbiology and Biotechnology·Cong T TrinhFriedrich Srienc
Apr 20, 2010·Journal of Bioinformatics and Computational Biology·Ali CakmakRichard W Hanson
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·A Ercument Cicek, Gultekin Ozsoyoglu
Aug 30, 2007·BMC Bioinformatics·Roland SchwarzThomas Dandekar
May 31, 2012·Algorithms for Molecular Biology : AMB·Sayed-Amir MarashiAlexander Bockmayr
Jul 1, 2008·BMC Systems Biology·Jeremiah Wright, Andreas Wagner
Apr 21, 2010·BMC Systems Biology·Isabel RochaMiguel Rocha
Nov 8, 2012·Briefings in Bioinformatics·Meiyappan LakshmananDong-Yup Lee
Jun 13, 2015·World Journal of Microbiology & Biotechnology·Predrag HorvatGerhart Braunegg
Mar 18, 2015·BMC Systems Biology·Pankaj NarangAndrew Michael Lynn
Mar 15, 2014·Briefings in Bioinformatics·Alberto RezolaFrancisco J Planes
Dec 10, 2020·Biotechnology & Genetic Engineering Reviews·Shreya AnandPadmini Padmanabhan

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Software Mentioned

MathSBML
Linux
MathType
SNAmat
PC
SNA
Matlab
SNAsym
Metatool
Mathematica

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