Michael Predl, Kilian Gandolf, Michael Hofer, Thomas Rattei
{"title":"ScyNet：可视化群落代谢模型中的相互作用","authors":"Michael Predl, Kilian Gandolf, Michael Hofer, Thomas Rattei","doi":"10.1093/bioadv/vbae104","DOIUrl":null,"url":null,"abstract":"<p><strong>Motivation: </strong>Genome-scale community metabolic models are used to gain mechanistic insights into interactions between community members. However, existing tools for visualizing metabolic models only cater to the needs of single organism models.</p><p><strong>Results: </strong>ScyNet is a Cytoscape app for visualizing community metabolic models, generating networks with reduced complexity by focusing on interactions between community members. ScyNet can incorporate the state of a metabolic model via fluxes or flux ranges, which is shown in a previously published simplified cystic fibrosis airway community model.</p><p><strong>Availability and implementation: </strong>ScyNet is freely available under an MIT licence and can be retrieved via the Cytoscape App Store (apps.cytoscape.org/apps/scynet). The source code is available at Github (github.com/univieCUBE/ScyNet).</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4000,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11315608/pdf/","citationCount":"0","resultStr":"{\"title\":\"ScyNet: Visualizing interactions in community metabolic models.\",\"authors\":\"Michael Predl, Kilian Gandolf, Michael Hofer, Thomas Rattei\",\"doi\":\"10.1093/bioadv/vbae104\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Motivation: </strong>Genome-scale community metabolic models are used to gain mechanistic insights into interactions between community members. However, existing tools for visualizing metabolic models only cater to the needs of single organism models.</p><p><strong>Results: </strong>ScyNet is a Cytoscape app for visualizing community metabolic models, generating networks with reduced complexity by focusing on interactions between community members. ScyNet can incorporate the state of a metabolic model via fluxes or flux ranges, which is shown in a previously published simplified cystic fibrosis airway community model.</p><p><strong>Availability and implementation: </strong>ScyNet is freely available under an MIT licence and can be retrieved via the Cytoscape App Store (apps.cytoscape.org/apps/scynet). The source code is available at Github (github.com/univieCUBE/ScyNet).</p>\",\"PeriodicalId\":72368,\"journal\":{\"name\":\"Bioinformatics advances\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2024-07-17\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11315608/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics advances\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/bioadv/vbae104\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbae104","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
ScyNet: Visualizing interactions in community metabolic models.
Motivation: Genome-scale community metabolic models are used to gain mechanistic insights into interactions between community members. However, existing tools for visualizing metabolic models only cater to the needs of single organism models.
Results: ScyNet is a Cytoscape app for visualizing community metabolic models, generating networks with reduced complexity by focusing on interactions between community members. ScyNet can incorporate the state of a metabolic model via fluxes or flux ranges, which is shown in a previously published simplified cystic fibrosis airway community model.
Availability and implementation: ScyNet is freely available under an MIT licence and can be retrieved via the Cytoscape App Store (apps.cytoscape.org/apps/scynet). The source code is available at Github (github.com/univieCUBE/ScyNet).
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