IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models

Abstract Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD databa...

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Autores principales:	Chao Ye, Nan Xu, Chuan Dong, Yuannong Ye, Xuan Zou, Xiulai Chen, Fengbiao Guo, Liming Liu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/26d78116c2144cd98197bed621f4aa7d
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spelling	oai:doaj.org-article:26d78116c2144cd98197bed621f4aa7d2021-12-02T11:52:22ZIMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models10.1038/s41598-017-00820-62045-2322https://doaj.org/article/26d78116c2144cd98197bed621f4aa7d2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00820-6https://doaj.org/toc/2045-2322Abstract Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.Chao YeNan XuChuan DongYuannong YeXuan ZouXiulai ChenFengbiao GuoLiming LiuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-9 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Chao Ye Nan Xu Chuan Dong Yuannong Ye Xuan Zou Xiulai Chen Fengbiao Guo Liming Liu IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
description	Abstract Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.
format	article
author	Chao Ye Nan Xu Chuan Dong Yuannong Ye Xuan Zou Xiulai Chen Fengbiao Guo Liming Liu
author_facet	Chao Ye Nan Xu Chuan Dong Yuannong Ye Xuan Zou Xiulai Chen Fengbiao Guo Liming Liu
author_sort	Chao Ye
title	IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
title_short	IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
title_full	IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
title_fullStr	IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
title_full_unstemmed	IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
title_sort	imgmd: a platform for the integration and standardisation of in silico microbial genome-scale metabolic models
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/26d78116c2144cd98197bed621f4aa7d
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IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models

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