Published by the Foundation for Open Access Statistics
Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks | Binsl | Journal of Statistical Software
Authors: Thomas W. Binsl, Katharine M. Mullen, Ivo H. M. van Stokkum, Jaap Heringa, Johannes H. G. M. van Beek
Title: FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks
Abstract: The representation of biochemical knowledge in terms of fluxes (transformation rates) in a metabolic network is often a crucial step in the development of new drugs and efficient bioreactors. Mass spectroscopy (MS) and nuclear magnetic resonance spectroscopy (NMRS) in combination with 13C labeled substrates are experimental techniques resulting in data that may be used to quantify fluxes in the metabolic network underlying a process. The massive amount of data generated by spectroscopic experiments increasingly requires software which models the dynamics of the underlying biological system. In this work we present an approach to handle isotopomer distributions in metabolic networks using an object-oriented programming approach, implemented using S4 classes in R. The developed package is called FluxSimulator and provides a user friendly interface to specify the topological information of the metabolic network as well as carbon atom transitions in plain text files. The package automatically derives the mathematical representation of the formulated network, and assembles a set of ordinary differential equations (ODEs) describing the change of each isotopomer pool over time. These ODEs are subsequently solved numerically. In a case study FluxSimulator was applied to an example network. Our results indicate that the package is able to reproduce exact changes in isotopomer compositions of the metabolite pools over time at given flux rates.

Page views:: 6094. Submitted: 2006-09-28. Published: 2007-01-10.
Paper: FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks     Download PDF (Downloads: 6073)
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DOI: 10.18637/jss.v018.i07

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Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.