CyREST

CyREST is a Cytoscape app that improves the reproducibility and productivity of bioinformatic workflows by allowing popular programming languages (such as Python and R) and tools (such as IPython/Jupyter Notebook and RStudio) to directly define and query networks, perform network analysis, layouts, and renderings. The app, along with harmonization libraries, enables researchers to automate Cytoscape-oriented tasks, making them less laborious and less prone to errors. CyREST's API and overall construction are described, and Python- and R-based examples are presented to illustrate how Cytoscape can be integrated into large scale data analysis pipelines. The tool is available for download on the Cytoscape app store and has been downloaded over 1900 times since its release in late 2014.