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Automating the PathLinker app for Cytoscape.

ABSTRACT: PathLinker 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.

SUBMITTER: Huang LJ

PROVIDER: S-EPMC6051191 | biostudies-other | 2018

REPOSITORIES: biostudies-other

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Automating the PathLinker app for Cytoscape.

Huang Li Jun LJ Law Jeffrey N JN Murali T M TM

F1000Research 20180612

PathLinker 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 softw ...[more]

PMID: 30057757

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