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Metabolites. 2017 Sep 6;7(3). pii: E47. doi: 10.3390/metabo7030047.

A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models.

Author information

1
Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany. alexandra.reimers@fu-berlin.de.
2
International Max Planck Research School for Computational Biology and Scientific Computing, Max Planck Institute for Molecular Genetics Berlin, 14195 Berlin, Germany. alexandra.reimers@fu-berlin.de.
3
Institute for Automation Engineering, Otto-von-Guericke-Universität Magdeburg, 39106 Magdeburg, Germany. henning.lindhorst@ovgu.de.
4
KU Leuven, Department of Chemical Engineering, 3001 Leuven, Belgium. steffen.waldherr@kuleuven.be.

Abstract

In this article, we present a protocol for generating a complete (genome-scale) metabolic resource allocation model, as well as a proposal for how to represent such models in the systems biology markup language (SBML). Such models are used to investigate enzyme levels and achievable growth rates in large-scale metabolic networks. Although the idea of metabolic resource allocation studies has been present in the field of systems biology for some years, no guidelines for generating such a model have been published up to now. This paper presents step-by-step instructions for building a (dynamic) resource allocation model, starting with prerequisites such as a genome-scale metabolic reconstruction, through building protein and noncatalytic biomass synthesis reactions and assigning turnover rates for each reaction. In addition, we explain how one can use SBML level 3 in combination with the flux balance constraints and our resource allocation modeling annotation to represent such models.

KEYWORDS:

SBML; constraint-based modeling; metabolic networks; optimality

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