SynBioEcoli： a comprehensive metabolism network of engineered E. coil in three dimensional visualization

• Published in: 中国电气与电子工程前沿：英文版 Vol. 5; no. 1; pp. 99 - 104
• Main Author: Weizhong Tu Shaozhen Ding Ling Wu Zhe Deng Hui Zhu Xiaotong Xu Chen Lin Chaonan Ye Minlu Han Mengna Zhao Juan Liu Zixin Deng Junni Chen Dong-Qing Wei Qian-Nan Hu
• Format: Journal Article
• Language: English
• Published: 2017
• ISSN: 2095-2732; 2095-2740

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 SynBioEcoll. Results： SynBioEoli contains 740 biosynthetic pathways, 3,889 metabolic reactions, 2,255 chemical compounds manually curated from about 11,000 metabolism publications related with different types of engineered E. coil 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/.