Under Cytoscape Automation, workflows can use CyREST to issue commands to Cytoscape and automation-enabled apps via the REST protocol, which encodes data as JSON documents. 1, Cytoscape Automation is a new Cytoscape feature that addresses these issues by extending the existing CyREST app, which empowers bioinformaticians to create reproducible workflows expressed in robust and well-known programming languages (e.g., Python, R, Javascript) using familiar programming environments (e.g., Jupyter and RStudio). Finally, as an interactive tool, Cytoscape is not positioned to add value to emerging workflows that integrate one or more external data acquisition and analysis tools (e.g., Galaxy, Taverna, and libraries provided in repositories such as PyPI and Bioconductor ).Īs shown in Fig. Moreover, while Cytoscape apps provide highly performant and relevant network biology functionality, the specialized programming talent and relatively long development times they require can make them uneconomical for delivering complex and evolving workflows. However, interactive use has proven inadequate for precisely reproducing or sharing complex analyses or for scaling to high volume or production analysis. Investigators can interactively explore complex *omics datasets via analysis and visualization functions provided by Cytoscape and a large and vibrant community of app contributors. As a platform for network biologic analysis, Cytoscape has proven to be enormously popular, with over 17,600 downloads worldwide each month, 5000 startups each day, and over 1000 direct citations per year.

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