Article (Scientific journals)
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
FLEMING, Ronan MT; THIELE, Ines
2011In Bioinformatics, 27 (1), p. 142-3
Peer reviewed
 

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Keywords :
Algorithms; Metabolism; Models, Biological; Software; Thermodynamics
Abstract :
[en] MOTIVATION: In flux balance analysis of genome scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady state mass conservation assumption and reaction directionality. Here, we introduce an algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the second law of thermodynamics to each reaction. Given experimental or computationally estimated standard metabolite species Gibbs energy and metabolite concentrations, the algorithms bounds reaction Gibbs energy, which is transformed to in vivo pH, temperature, ionic strength and electrical potential. RESULTS: This cross-platform MATLAB extension to the COnstraint-Based Reconstruction and Analysis (COBRA) toolbox is computationally efficient, extensively documented and open source. AVAILABILITY: http://opencobra.sourceforge.net.
Disciplines :
Life sciences: Multidisciplinary, general & others
External co-authors :
yes
Language :
English
Title :
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
Publication date :
2011
Journal title :
Bioinformatics
ISSN :
1367-4803
eISSN :
1367-4811
Volume :
27
Issue :
1
Pages :
142-3
Peer reviewed :
Peer reviewed
Available on ORBilu :
since 30 April 2014

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