Automating the PathLinker app for Cytoscape

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dc.contributor.authorHuang, Li Junen
dc.contributor.authorLaw, Jeffrey N.en
dc.contributor.authorMurali, T. M.en
dc.date.accessioned2020-11-03T14:26:58Zen
dc.date.available2020-11-03T14:26:58Zen
dc.date.issued2018-06-12en
dc.description.abstractPathLinker is a graph-theoretic algorithm originally developed to reconstruct the interactions in a signaling pathway of interest. It efficiently computes multiple short paths within a background protein interaction network from the receptors to transcription factors (TFs) in a pathway. Since December 2015, PathLinker has been available as an app for Cytoscape. This paper describes how we automated the app to use the CyRest infrastructure and how users can incorporate PathLinker into their software pipelines.en
dc.description.sponsorshipNational Science Foundation grant [CCF-1617678] supported this research. The research is also partially based upon work supported by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), via the Army Research Office (ARO) under cooperative Agreement Number [W911NF-17-2-0105].en
dc.format.extent9 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationHuang LJ, Law JN and Murali TM. Automating the PathLinker app for Cytoscape [version 1; peer review: 2 approved] F1000Research 2018, 7:727 https://doi.org/10.12688/f1000research.14616.1en
dc.identifier.doihttps://doi.org/10.12688/f1000research.14616.1en
dc.identifier.issue727en
dc.identifier.urihttp://hdl.handle.net/10919/100777en
dc.identifier.volume7en
dc.language.isoenen
dc.publisherF1000Researchen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectNetwork Biologyen
dc.subjectShortest Pathsen
dc.subjectPathway Reconstructionen
dc.subjectCyREST APIen
dc.titleAutomating the PathLinker app for Cytoscapeen
dc.title.serialF1000Researchen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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