Journal
COMPUTERS IN BIOLOGY AND MEDICINE
Volume 105, Issue -, Pages 64-71Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.compbiomed.2018.12.010
Keywords
Systems biology; Metabolic networks; Flux balance analysis; Computational modeling; Metabolic engineering
Categories
Funding
- United States Department of Defense [W81XWH-14-C-0054]
- National Science Foundation Graduate Research Fellowship Program
- National Science Foundation Multi-scale Systems Bioengineering Research Experience for Undergraduates
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GEnome-scale Network REconstructions (GENREs) mathematically describe metabolic reactions of an organism or a specific cell type. GENREs can be used with a number of constraint-based reconstruction and analysis (COBRA) methods to make computational predictions on how a system changes in different environments. We created a simplified GENRE (referred to as iSIM) that captures central energy metabolism with nine metabolic reactions to illustrate the use of and promote the understanding of GENREs and constraint-based methods. We demonstrate the simulation of single and double gene deletions, flux variability analysis (FVA), and test a number of metabolic tasks with the GENRE. Code to perform these analyses is provided in Python, R, and MATLAB. Finally, with iSIM as a guide, we demonstrate how inaccuracies in GENREs can limit their use in the interrogation of energy metabolism.
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