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As part of our Cytoscape Apps gateway, we are excited to launch the Cytoscape Automation collection – with the support of Alexander Pico (UCSF), Barry Demchak (UCSD School of Medicine), and William Longabaugh (Institute for Systems Biology). The collection features 10 articles that describe new callable functionality exposed in a number of highly used Cytoscape apps, each written by the app authors themselves.

For those who are not familiar with this new initiative, Cytoscape Automation enables scripting languages (e.g., Python, R or Javascript) to call Cytoscape functions. This means that Cytoscape users can create reproducible workflows. In order to ensure that these new automations serve as a resource to researchers and app developers, each article includes an explanation of the newly available function(s), how the function(s) can be called, and real-world applications.

A good example of this is the new eXamine automation feature, developed by Philipp Sporh and colleagues from Heinrich Heine University. This automation enables researchers to compose reproducible analysis workflows that generate visualisations of small, set-annotated graphs. The paper includes two use cases as handy Jupyter notebooks, which peer reviewer Markus List (Technical University Munich) stated are well described and “illustrate to the user how eXamine can be used in a scripting environment such as Python”.

Mohammed El-Kebir, University of Illinois at Urbana-Champaign, last author of the eXamine article, sees significant value in sharing this work as part of the collection:

“Scientific progress in data-driven fields hinges on reproducibility of results. To enable reproducibility, researchers need to be incentivised to make their methods amenable for use in computational workflows. The Cytoscape Automation collection takes an important step in this direction.”

In short, quoting the editorial from Barry Demchak and colleagues: “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.” And indeed it seems the collection is already in use by the wider Cytoscape community. Ruth Isserlin, University of Toronto, is an automation user and she describes how the collection is of use to her work:

“Integrating Cytoscape into my RNotebook pipelines makes my analyses automatable, reproducible and reusable from start to finish. Rcy3 has made this process easy and efficient. The F1000Research Cytoscape Automation collection makes finding new Apps to incorporate into my pipelines much easier.”