ArticleMetabolites2017
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models.
Article in Metabolites, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Systems biology and microbiome innovations for personalized diabetic retinopathy management.NPJ systems biology and applications · 2025Review
- Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.Metabolites · 2024Review
- A study of a diauxic growth experiment using an expanded dynamic flux balance framework.PloS one · 2023Article
- Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.Annual review of biomedical engineering · 2021Review
- Development of a Genome-Scale Metabolic Model ofFrontiers in bioengineering and biotechnology · 2020Article
- Constraint-based modeling in microbial food biotechnology.Biochemical Society transactions · 2018Review
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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