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Editorial

The Cytoscape Automation app article collection

[version 1; peer review: not peer reviewed]
PUBLISHED 20 Jun 2018
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This article is included in the Cytoscape gateway.

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

Cytoscape, Automation, App, Network Biology, Network Analysis, Network Visualization

Editorial

Cytoscape is an open source software platform for interactive analysis, integration and visualization of networks and network data1. At heart, Cytoscape provides basic network analysis functionality (e.g., network import/export, network data analysis, visualization and layout) in a menu-driven desktop format. Most importantly, it also enables and encourages users to add extensions (called apps) that deliver custom features important for specific workflows (e.g., ClueGO2 for enrichment analysis relative to various ontologies). To date, Cytoscape users can choose among over 330 apps written by over 550 authors.

In 2014, the CyREST app3 was created to allow external programs to exercise core Cytoscape functionality as part of custom workflows. By authoring such workflows in common languages (such as R and Python), users can combine the best features of Cytoscape with those available in language-specific libraries, thus creating new value much more quickly and cheaply than writing conventional Cytoscape apps. Furthermore, such workflows can more easily integrate external applications (e.g., GenePattern and iGraph) and multiple large datasets. Finally, external workflows enable reproducibility not available using Cytoscape’s standard mouse/keyboard/display interaction mode.

In 2018, Cytoscape Automation was created to enable external workflows to also call functionality in apps. For an app to be callable, it must be upgraded to support automation via either a Commands or Functions interface. As of March, 2018, app authors upgraded and released 22 apps.

This collection of Cytoscape app articles at F1000Research is intended to serve as a resource to researchers (as workflow authors) and app developers to understand the features and interfaces exposed by automation-enabled apps. They are written by the app authors themselves according to a template that calls for explaining newly available functions, how they can be called, and with real world examples. We intend that readers be able to quickly and economically incorporate Cytoscape app functionality as reproducible workflows that scale independently to large data sets and production runs.

Data availability

No data are associated with this article.

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Version 1
VERSION 1 PUBLISHED 20 Jun 2018
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Demchak B, Otasek D, Pico AR et al. The Cytoscape Automation app article collection [version 1; peer review: not peer reviewed]. F1000Research 2018, 7:800 (https://doi.org/10.12688/f1000research.15355.1)
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Open Peer Review

Current Reviewer Status:
NOT PEER REVIEWED
NOT PEER REVIEWED

Comments on this article Comments (0)

Version 1
VERSION 1 PUBLISHED 20 Jun 2018
Comment
Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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