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The MONGOOSE Rational Arithmetic Toolbox

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Metabolic Network Reconstruction and Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1716))

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Abstract

The modeling of metabolic networks has seen a rapid expansion following the complete sequencing of thousands of genomes. The constraint-based modeling framework has emerged as one of the most popular approaches to reconstructing and analyzing genome-scale metabolic models. Its main assumption is that of a quasi-steady-state, requiring that the production of each internal metabolite be balanced by its consumption. However, due to the multiscale nature of the models, the large number of reactions and metabolites, and the use of floating-point arithmetic for the stoichiometric coefficients, ensuring that this assumption holds can be challenging.

The MONGOOSE toolbox addresses this problem by using rational arithmetic, thus ensuring that models are analyzed in a reproducible manner and consistently with modeling assumptions. In this chapter we present a protocol for the complete analysis of a metabolic network model using the MONGOOSE toolbox, via its newly developed GUI, and describe how it can be used as a model-checking platform both during and after the model construction process.

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Acknowledgements

The authors would like to thank Dan Park for creating the MONGOOSE website. In addition, the authors would like to acknowledge the invaluable input of Bonnie Berger, Aviv Regev, and Jason Trigg, as well as the help of Daniel Espinoza and Dan Steffy. This work is supported by an NSERC Discovery Grant as well as an Alfred P. Sloan Fellowship.

Author information

Authors and Affiliations

  1. School of Computing Sciences, Simon Fraser University, Burnaby, BC, Canada

    Leonid Chindelevitch

  2. School of Computing Sciences, Simon Fraser University, Burnaby, BC, Canada

    Christopher Le

Authors
  1. Christopher Le
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  2. Leonid Chindelevitch
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Corresponding author

Correspondence to Leonid Chindelevitch .

Editor information

Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

    Marco Fondi

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Le, C., Chindelevitch, L. (2018). The MONGOOSE Rational Arithmetic Toolbox. In: Fondi, M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7528-0_3

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  • DOI: https://doi.org/10.1007/978-1-4939-7528-0_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7527-3

  • Online ISBN: 978-1-4939-7528-0

  • eBook Packages: Springer Protocols

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