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Biol."],"published-print":{"date-parts":[[2017,3]]},"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>A comprehensive metabolism network of engineered <jats:italic>E. coli<\/jats:italic> is very important in systems biology and metabolomics studies. Many tools focus on two\u2010dimensional space to display pathways in metabolic network. However, the usage of three\u2010dimensional visualization may help to understand better the intricate topology of metabolic and regulatory networks.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We manually curated large amount of experimental data (including pathways, reactions and metabolites) from literature related with different types of engineered <jats:italic>E. coli<\/jats:italic> and then utilized a novel technology of three dimensional visualization to develop a comprehensive metabolic network named SynBioEcoli.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>SynBioEoli contains 740 biosynthetic pathways, 3,889\u00a0metabolic reactions, 2,255 chemical compoundsmanually curated from about 11,000\u00a0metabolism publications related with different types of engineered <jats:italic>E. coli<\/jats:italic>. Furthermore, SynBioEcoli integrates with various informatics techniques.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>SynBioEcoli could be regarded as a comprehensive knowledgebase of engineered <jats:italic>E. coli<\/jats:italic> and represents the next generation cellular metabolism network visualization technology. It could be accessed via web browsers (such as Google Chrome) supporting WebGL, at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.rxnfinder.org\/synbioecoli\/\">http:\/\/www.rxnfinder.org\/synbioecoli\/<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1007\/s40484-017-0098-1","type":"journal-article","created":{"date-parts":[[2017,3,17]],"date-time":"2017-03-17T09:06:05Z","timestamp":1489741565000},"page":"99-104","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["SynBioEcoli: a comprehensive metabolism network of engineered <i><b>E. coli<\/b><\/i> in three dimensional visualization"],"prefix":"10.1002","volume":"5","author":[{"given":"Weizhong","family":"Tu","sequence":"first","affiliation":[{"name":"<!--2--> Wuhan LifeSynther Cooperation Limited Wuhan 430078 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