Reference : von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabol...
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/16518
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
English
Fleming, Ronan MT mailto [> >]
Thiele, Ines mailto [> >]
2011
Bioinformatics (Oxford, England)
27
1
142-3
Yes (verified by ORBilu)
1367-4803
1367-4811
England
[en] Algorithms ; Metabolism ; Models, Biological ; Software ; Thermodynamics
[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.
http://hdl.handle.net/10993/16518
10.1093/bioinformatics/btq607

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