期刊
BIOINFORMATICS
卷 27, 期 1, 页码 142-143出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btq607
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资金
- National Institute of Health [5R01GM057089-11]
- United States Department of Energy, Offices of Advanced Scientific Computing Research
- Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program [DE-SC0002009]
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM057089] Funding Source: NIH RePORTER
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.
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