Abstract:
:Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for example, Python/R in Jupyter/RStudio. We expose over 270 Cytoscape core functions and 34 Cytoscape apps as REST-callable functions with standardized JSON interfaces backed by Swagger documentation. Independent projects to create and publish Python/R native CA interface libraries have reached an advanced stage, and a number of automation workflows are already published.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Otasek D,Morris JH,Bouças J,Pico AR,Demchak Bdoi
10.1186/s13059-019-1758-4subject
Has Abstractpub_date
2019-09-02 00:00:00pages
185issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-019-1758-4journal_volume
20pub_type
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