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Editorial
. 2018 Jun 20:7:800.
doi: 10.12688/f1000research.15355.1. eCollection 2018.

The Cytoscape Automation app article collection

Barry Demchak  1 , David Otasek  1 , Alexander R Pico  2 , Gary D Bader  3 , Keiichiro Ono  1 , Brett Settle  1 , Eric Sage  1 , John H Morris  4 , William Longabaugh  5 , Christian Lopes  3 , Michael Kucera  3 , Adam Treister  2 , Benno Schwikowski  6 , Piet Molenaar  7 , Trey Ideker  1
Affiliations
Editorial

The Cytoscape Automation app article collection

Barry Demchak et al. F1000Res. .

Abstract

Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic functionality, it relies on community-written apps to deliver specialized functions and analyses. To date, Cytoscape's CyREST feature has allowed researchers to write workflows that call basic Cytoscape functions, but provides no access to its high value app-based functions. With Cytoscape Automation, workflows can now call apps that have been upgraded to expose their functionality. This article collection is a resource to assist readers in quickly and economically leveraging such apps in reproducible workflows that scale independently to large data sets and production runs.

Keywords: App; Automation; Cytoscape; Network Analysis; Network Biology; Network Visualization.

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Conflict of interest statement

No competing interests were disclosed.

References

    1. Pico AR, Bader GD, Demchak B, et al. : The Cytoscape app article collection [version 1; referees: not peer reviewed]. F1000Res. 2014;3:138. 10.12688/f1000research.4642.1 - DOI - PMC - PubMed
    1. Bindea G, Mlecnik B, Hackl H, et al. : ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091–1093. 10.1093/bioinformatics/btp101 - DOI - PMC - PubMed
    1. Ono K, Muetze T, Kolishovski G, et al. : CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API [version 1; referees: 2 approved]. F1000Res. 2015;4:478. 10.12688/f1000research.6767.1 - DOI - PMC - PubMed

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