Open AccessSynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization
Author(s) -
Tu Weizhong,
Ding Shaozhen,
Wu Ling,
Deng Zhe,
Zhu Hui,
Xu Xiaotong,
Lin Chen,
Ye Chaonan,
Han Minlu,
Zhao Mengna,
Liu Juan,
Deng Zixin,
Chen Junni,
Wei DongQing,
Hu QianNan
Publication year - 2017
Publication title -
quantitative biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.707
H-Index - 15
eISSN - 2095-4697
pISSN - 2095-4689
DOI - 10.1007/s40484-017-0098-1
Subject(s) - visualization , metabolic network , computer science , systems biology , synthetic biology , metabolic engineering , cellular metabolism , metabolic pathway , computational biology , informatics , data science , biology , metabolism , data mining , biochemistry , engineering , electrical engineering , enzyme
Background A comprehensive metabolism network of engineered E. coli is very important in systems biology and metabolomics studies. Many tools focus on two‐dimensional space to display pathways in metabolic network. However, the usage of three‐dimensional visualization may help to understand better the intricate topology of metabolic and regulatory networks. Methods We manually curated large amount of experimental data (including pathways, reactions and metabolites) from literature related with different types of engineered E. coli and then utilized a novel technology of three dimensional visualization to develop a comprehensive metabolic network named SynBioEcoli. Results SynBioEoli contains 740 biosynthetic pathways, 3,889 metabolic reactions, 2,255 chemical compoundsmanually curated from about 11,000 metabolism publications related with different types of engineered E. coli . Furthermore, SynBioEcoli integrates with various informatics techniques. Conclusions SynBioEcoli could be regarded as a comprehensive knowledgebase of engineered E. coli and represents the next generation cellular metabolism network visualization technology. It could be accessed via web browsers (such as Google Chrome) supporting WebGL, at http://www.rxnfinder.org/synbioecoli/ .