{"title":"合成代谢途径解空间分析","authors":"J. Meitalovs, E. Stalidzans","doi":"10.1109/ICSSE.2013.6614656","DOIUrl":null,"url":null,"abstract":"The size and the number of available genome scale metabolic models and reconstructions of different organisms is growing rapidly. Various computational methods and tools are developed in the last decades for metabolic network construction, analysis and optimization in the interdisciplinary scientific branches of systems biology and synthetic biology. A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of pathways to new metabolites. The necessary time for a metabolic pathway supergraph development using reactions from KEGG database is analyzed. The construction of all the up to 15 reactions long pathways for glucose, glycerol and xylose takes about 11 000 seconds involving about 5500 metabolites from totally 17 000 available metabolites in the KEGG data base. Availability: www.biosystems.lv/sanalyzer.","PeriodicalId":124317,"journal":{"name":"2013 International Conference on System Science and Engineering (ICSSE)","volume":"47 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2013-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"3","resultStr":"{\"title\":\"Analysis of synthetic metabolic pathways solution space\",\"authors\":\"J. Meitalovs, E. Stalidzans\",\"doi\":\"10.1109/ICSSE.2013.6614656\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The size and the number of available genome scale metabolic models and reconstructions of different organisms is growing rapidly. Various computational methods and tools are developed in the last decades for metabolic network construction, analysis and optimization in the interdisciplinary scientific branches of systems biology and synthetic biology. A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of pathways to new metabolites. The necessary time for a metabolic pathway supergraph development using reactions from KEGG database is analyzed. The construction of all the up to 15 reactions long pathways for glucose, glycerol and xylose takes about 11 000 seconds involving about 5500 metabolites from totally 17 000 available metabolites in the KEGG data base. Availability: www.biosystems.lv/sanalyzer.\",\"PeriodicalId\":124317,\"journal\":{\"name\":\"2013 International Conference on System Science and Engineering (ICSSE)\",\"volume\":\"47 1\",\"pages\":\"0\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2013-07-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"3\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"2013 International Conference on System Science and Engineering (ICSSE)\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/ICSSE.2013.6614656\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"2013 International Conference on System Science and Engineering (ICSSE)","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/ICSSE.2013.6614656","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Analysis of synthetic metabolic pathways solution space
The size and the number of available genome scale metabolic models and reconstructions of different organisms is growing rapidly. Various computational methods and tools are developed in the last decades for metabolic network construction, analysis and optimization in the interdisciplinary scientific branches of systems biology and synthetic biology. A software tool SpaceAnalyzer (SAnalyzer) is developed in Matlab environment for automatic generation of pathways to new metabolites. The necessary time for a metabolic pathway supergraph development using reactions from KEGG database is analyzed. The construction of all the up to 15 reactions long pathways for glucose, glycerol and xylose takes about 11 000 seconds involving about 5500 metabolites from totally 17 000 available metabolites in the KEGG data base. Availability: www.biosystems.lv/sanalyzer.
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