Cargando…
IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
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 bu...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429687/ https://www.ncbi.nlm.nih.gov/pubmed/28389638 http://dx.doi.org/10.1038/s41598-017-00820-6 |
_version_ | 1783236077061931008 |
---|---|
author | Ye, Chao Xu, Nan Dong, Chuan Ye, Yuannong Zou, Xuan Chen, Xiulai Guo, Fengbiao Liu, Liming |
author_facet | Ye, Chao Xu, Nan Dong, Chuan Ye, Yuannong Zou, Xuan Chen, Xiulai Guo, Fengbiao Liu, Liming |
author_sort | Ye, Chao |
collection | PubMed |
description | 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 | Online Article Text |
id | pubmed-5429687 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-54296872017-05-15 IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models Ye, Chao Xu, Nan Dong, Chuan Ye, Yuannong Zou, Xuan Chen, Xiulai Guo, Fengbiao Liu, Liming Sci Rep Article 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. Nature Publishing Group UK 2017-04-07 /pmc/articles/PMC5429687/ /pubmed/28389638 http://dx.doi.org/10.1038/s41598-017-00820-6 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Ye, Chao Xu, Nan Dong, Chuan Ye, Yuannong Zou, Xuan Chen, Xiulai Guo, Fengbiao Liu, Liming IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models |
title | 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_short | 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 |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429687/ https://www.ncbi.nlm.nih.gov/pubmed/28389638 http://dx.doi.org/10.1038/s41598-017-00820-6 |
work_keys_str_mv | AT yechao imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels AT xunan imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels AT dongchuan imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels AT yeyuannong imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels AT zouxuan imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels AT chenxiulai imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels AT guofengbiao imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels AT liuliming imgmdaplatformfortheintegrationandstandardisationofinsilicomicrobialgenomescalemetabolicmodels |