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Demchak B, Otasek D, Pico AR, et al. The Cytoscape Automation app article collection. F1000Res. 2018;7:800doi: 10.12688/f1000research.15355.1.
Demchak, B., Otasek, D., Pico, A. R., Bader, G. D., Ono, K., Settle, B., Sage, E., Morris, J. H., Longabaugh, W., Lopes, C., Kucera, M., Treister, A., Schwikowski, B., Molenaar, P., & Ideker, T. (2018). The Cytoscape Automation app article collection. F1000Research, 7800. https://doi.org/10.12688/f1000research.15355.1
Demchak, Barry, et al. "The Cytoscape Automation app article collection." F1000Research vol. 7 (2018): 800. doi: https://doi.org/10.12688/f1000research.15355.1
Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collection. F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. PMID: 29983926; PMCID: PMC6013757.
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F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018.

The Cytoscape Automation app article collection.

F1000Research

Barry Demchak, David Otasek, Alexander R Pico, Gary D Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H Morris, William Longabaugh, Christian Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, Trey Ideker

Affiliations

  1. Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
  2. Gladstone Institutes, San Francisco, CA, 95158, USA.
  3. The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.
  4. University of California, San Francisco, San Francisco, CA, 94143, USA.
  5. Institute for Systems Biology, Seattle, WA, 98109, USA.
  6. Inistitut Pasteur, Paris, 75015, France.
  7. Amsterdam Medical Centre, Ansterdam, 1105 AZ, Netherlands.

PMID: 29983926 PMCID: PMC6013757 DOI: 10.12688/f1000research.15355.1

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

Conflict of interest statement

No competing interests were disclosed.

References

  1. Bioinformatics. 2009 Apr 15;25(8):1091-3 - PubMed
  2. F1000Res. 2014 Jul 01;3:138 - PubMed
  3. F1000Res. 2015 Aug 05;4:478 - PubMed

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Grant support