The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

By Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen. PLoS Comput. Biol., 2013

391 citations recorded by the source corpus.

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 chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/867a304c64f26f5eddebf50a41c3d75cc5071de8

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Citations in the corpus

COBRApy: COnstraints-Based Reconstruction and Analysis for Python (2013, methodology): “In recent years, a number of software packages have been developed that employ stoichiometric constraint-based modeling approaches [23], such as Cell Net Analyzer [24], FASIMU [25], PySCeS-CBM [26], the Raven Toolbox [27], and the Systems Biology Research Tool [28].”
antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters (2015, methodology): “In addition, a prototype functionality has been added for the automated generation of prokaryotic draft genome-scale metabolic models, following the established approach of homology-based modeling (14).”
Using Genome-Scale Models to Predict Biological Capabilities (2015, neutral): “…of gen ome-scale re constructions (some-times called GENREs) for a number of target organisms (Monk et al., 2014; Oberhardt et al., 2011), and established protocols for reconstruction exist (Thiele and Palsson, 2010) that can be partially automated (Agren et al., 2013; Henry et al., 2010a).”
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor (2018, methodology): “The RAVEN Toolbox 1.0 was released as an open-source MATLAB-package [9], that has since seen minor updates and bugfixes.”
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities (2018, background): “Several metabolic reconstruction tools are currently available, each offering different degrees of trade-off between automation and human intervention [20, 21, 22, 23].”
Insights from 20 years of bacterial genome sequencing (2015, methodology): “There are other software platforms that are tailor made for semi-automated GEMs reconstruction like the Raven toolbox (Agren et al. 2013) which has a Web-based version (GarciaAlbornoz et al.”