Automating the PathLinker app for Cytoscape

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Date

2018-06-12

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Journal ISSN

Volume Title

Publisher

F1000Research

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.

Description

Keywords

Network Biology, Shortest Paths, Pathway Reconstruction, CyREST API

Citation

Huang 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.14616.1

Persistent link

http://hdl.handle.net/10919/100777

Collections

Scholarly Works, Computer Science
Scholarly Works, Institute for Critical Technology and Applied Science (ICTAS)