A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models
1
Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
2
International Max Planck Research School for Computational Biology and Scientific Computing, Max Planck Institute for Molecular Genetics Berlin, 14195 Berlin, Germany
3
Institute for Automation Engineering, Otto-von-Guericke-Universität Magdeburg, 39106 Magdeburg, Germany
4
KU Leuven, Department of Chemical Engineering, 3001 Leuven, Belgium
*
Authors to whom correspondence should be addressed.
Metabolites 2017, 7(3), 47; https://doi.org/10.3390/metabo7030047
Received: 28 July 2017
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Revised: 30 August 2017
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Accepted: 4 September 2017
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Published: 6 September 2017
(This article belongs to the Special Issue Metabolism and Systems Biology Volume 2)
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.
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Keywords:
constraint-based modeling; optimality; metabolic networks; SBML
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MDPI and ACS Style
Reimers, A.-M.; Lindhorst, H.; Waldherr, S. A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. Metabolites 2017, 7, 47. https://doi.org/10.3390/metabo7030047
AMA Style
Reimers A-M, Lindhorst H, Waldherr S. A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. Metabolites. 2017; 7(3):47. https://doi.org/10.3390/metabo7030047
Chicago/Turabian StyleReimers, Alexandra-M., Henning Lindhorst, and Steffen Waldherr. 2017. "A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models" Metabolites 7, no. 3: 47. https://doi.org/10.3390/metabo7030047
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