The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.

ABSTRACT: We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium ch

SUBMITTER: Agren R 

PROVIDER: S-EPMC3605104 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature