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Mathematical Framework Behind the Reconstruction and Analysis of Genome Scale Metabolic Models

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Abstract

Scale Metabolic Models (GEMs) emerged as a formal concept to describe metabolic pathways reconstructed from the information present in the genome of living systems as well as in the biochemical reactions described in the literature. This formalization involves steps including determination of their stoichiometry and definition of model constraints. Genome Scale Metabolic Models (GEMs) are mathematically structured knowledge that can be used to generate and test biological hypotheses when integrated with experimental data. Recently the community started to recognize the potential of GEMS and their analysis with constraint-based modeling. Therefore, when using GEMs for applications including in silico metabolic engineering, it´s important to understand the assumption behind its mathematical framework, but usually the theory behind is not accessible to a broad audience in one place. This work aims to present a concise theoretical and practical introduction to GEMS that is accessible to a broad audience getting them closer to the use and applications of GEMS.

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Acknowledgements

This work was supported by Universidad San Buenaventura (Engineering faculty) and Pontificia Universidad Javeriana, Grants 7740, 7714 and 7425 to J. González.

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Authors and Affiliations

  1. Universidad San Buenaventura, Bogotá, D.C., Colombia

    W. Pinzon & H. Vega

  2. Laboratorio de Bioquímica Computacional Estructural y Bioinformática, Pontificia Universidad Javeriana, Bogotá, D.C., Colombia

    J. Gonzalez

  3. Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá, D.C., Colombia

    A. Pinzon

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  1. W. Pinzon
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  2. H. Vega
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Correspondence to J. Gonzalez.

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Pinzon, W., Vega, H., Gonzalez, J. et al. Mathematical Framework Behind the Reconstruction and Analysis of Genome Scale Metabolic Models. Arch Computat Methods Eng 26, 1593–1606 (2019). https://doi.org/10.1007/s11831-018-9290-3

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  • DOI: https://doi.org/10.1007/s11831-018-9290-3

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