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The Cytoscape Gateway has been a staple of the F1000Research bioinformatic landscape since launching in 2014. Here, Tom Sinden (Publishing Executive, F1000) shares new details about the Gateway’s recently expanded scope and looks back on some of the most important research to date.

What is the Cytoscape Gateway?

Cytoscape is an open-source software platform for network visualization, data integration, and network analysis. Researchers mainly use Cytoscape for molecular networks and pathways in biology. However, many also use the platform to interrogate the entire range from atomic and residue interactions in protein structures to chromosomal, cellular, organismal, and social networks. Significantly, Cytoscape also has non-biological applications.

The Cytoscape Gateway is a tailored publication hub for new developments in the Cytoscape landscape.

Expanding the Gateway’s scope

The Cytoscape Gateway has published many articles with tens of thousands of views and downloads between them. To reflect the development of the Cytoscape platform over this period, we have updated the Gateway’s scope to encompass a greater variety of article topics. In addition to the existing Software Tool articles that highlight Java-based Cytoscape Apps, the Gateway will also include technical extensions written using R or Python. Moreover, authors are now able to submit Study Protocols and Method Articles involving the broader Cytoscape ecosystem.

As we look forward to the evolution of the Cytoscape Gateway, here’s a look at just some of the content that has helped shape this hub over the past seven years.

Most Views and Downloads

KEGGscape: a Cytoscape app for pathway data integration

Kozo Nishida, Keiichiro Ono, Shigehiko Kanaya & Koichi Takahashi

 This article has amassed over 13,000 views across F1000Research and PubMed Central. As a result, it is currently the most viewed output on the Gateway. The content grants an introduction to the KEGGscape App, which uses the KEGG biological database to create a pathway data integration and visualization app for the Cytoscape community.

ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis

Guanming Wu, Eric Dawson, Adrian Duong, Robin Haw & Lincoln Stein

With over 1,600 downloads on F1000Research alone, this Software Tool article introduces the ReactomeFIViz app. The app offers several different features to aid users in performing pathway- and network-based data analysis intuitively.

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Publisher’s Pick

netDx: Software for building interpretable patient classifiers by multi-‘omic data integration using patient similarity networks

Shraddha Pai, Philipp Weber, Ruth Isserlin, Hussam Kaka, Shirley Hui, Muhammad Ahmad Shah, Luca Giudice, Rosalba Giugno, Anne Krogh Nøhr, Jan Baumbach & Gary D. Bader

This article is an excellent example of the synergy that can exist between complementary bioinformatic tools. It uses the resources of both Bioconductor and Cytoscape to develop a novel workflow for building pathway-based patient classifiers. I’m confident that it will continue to serve as a valuable guide to the bioinformatics community.

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Community Choice

RCy3: Network biology using Cytoscape from within R

 Julia A. Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico

 “In addition to articles on specific Cytoscape apps, the Gateway also highlights new technology broadly relevant to the network biology community, like the RCy3 package. RCy3 is a top-200 R package in Bioconductor that brings the functionality of Cytoscape (and many apps) to the R environment via the CyREST API. In this article, we describe the organization of the R package, provide use cases, and show how RCy3 connects to over 30 other Bioconductor packages involving network objects.”

 — Alex Pico, Cytoscape Gateway Advisor

We’re incredibly excited to welcome submissions to the newly expanded Cytoscape Gateway. For the complete scope, please visit the Gateway homepage.

If you’ve produced a new Cytoscape App, extension, or methodology, we invite you to share your work with the broader research community. We also encourage you to submit any posters or slides to the Gateway. Submit your research today or get in touch with any questions.