A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models
AbstractIn 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. View Full-Text
- Supplementary File 1:
ZIP-Document (ZIP, 134 KB)
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Reimers, A.-M.; Lindhorst, H.; Waldherr, S. A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. Metabolites 2017, 7, 47.
Reimers A-M, Lindhorst H, Waldherr S. A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. Metabolites. 2017; 7(3):47.Chicago/Turabian Style
Reimers, Alexandra-M.; Lindhorst, Henning; Waldherr, Steffen. 2017. "A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models." Metabolites 7, no. 3: 47.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.