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

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 fe...

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Autores principales:	Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/ca24dcf395d148a8bc5202a83cdc1a31
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spelling	oai:doaj.org-article:ca24dcf395d148a8bc5202a83cdc1a312021-11-18T05:52:19ZThe RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.1553-734X1553-735810.1371/journal.pcbi.1002980https://doaj.org/article/ca24dcf395d148a8bc5202a83cdc1a312013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23555215/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358We 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.Rasmus AgrenLiming LiuSaeed ShoaieWanwipa VongsangnakIntawat NookaewJens NielsenPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 3, p e1002980 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Rasmus Agren Liming Liu Saeed Shoaie Wanwipa Vongsangnak Intawat Nookaew Jens Nielsen The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
description	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.
format	article
author	Rasmus Agren Liming Liu Saeed Shoaie Wanwipa Vongsangnak Intawat Nookaew Jens Nielsen
author_facet	Rasmus Agren Liming Liu Saeed Shoaie Wanwipa Vongsangnak Intawat Nookaew Jens Nielsen
author_sort	Rasmus Agren
title	The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
title_short	The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
title_full	The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
title_fullStr	The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
title_full_unstemmed	The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.
title_sort	raven toolbox and its use for generating a genome-scale metabolic model for penicillium chrysogenum.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/ca24dcf395d148a8bc5202a83cdc1a31
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The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.

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