The Cytoscape Automation app article collection

Barry Demchak (1) , David Otasek (1) , Alexander 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 Kuchera (3) , Adam Treister (2) , Benno Schwikowski (6) , Piet Molenaar (7) , Trey Ideker (1)

1 UC San Diego - University of California [San Diego]
2 Gladstone Institutes [San Francisco]
3 Donnelly Centre [Toronto, ON, Canada]
4 UC San Francisco - University of California [San Francisco]
5 Institute for Systems Biology [Seattle, WA, USA]
6 Biologie systémique - Systems Biology
7 AMC - Academic Medical Center - Academisch Medisch Centrum [Amsterdam]

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

Domains: Computer Science [cs]; Bioinformatics [q-bio.QM]

Barry Demchak, David Otasek, Alexander Pico, Gary D Bader, Keiichiro Ono, et al.. The Cytoscape Automation app article collection. F1000Research, 2018, 7, pp.800. ⟨10.12688/f1000research.15355.1⟩. ⟨pasteur-02972651⟩