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

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 rat

SUBMITTER: Reimers AM 

PROVIDER: S-EPMC5618332 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature