dot-app: a Graphviz-Cytoscape conversion plug-in [version 2; referees: 3 approved, 1 approved with reservations]

• Main Authors: Braxton Fitts, Ziran Zhang, Massoud Maher, Barry Demchak
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2017-07-01
• Series: F1000Research
• Subjects: Bioinformatics
• Online Access: https://f1000research.com/articles/5-2543/v2

dot-app is a Cytoscape 3 app that allows Cytoscape to import and export Graphviz (.dot, .gv) files, also known as DOT files due to the .dot extension and their conformance to the DOT language syntax. The DOT format was originally created in the early 2000s to represent graph topologies, layouts and formatting. DOT-encoded files are produced and consumed by a number of open-source graph applications, including Graphviz, Gephi, Tulip, and others. While DOT-based graph applications are popular, they emphasize general graph layout and styling over the topological and semantic analysis functions available in domain-focused applications such as Cytoscape. While domain-focused applications have easy access to large networks (10,000 to 100,000 nodes) and advanced analysis and formatting, they do not have as many styling options as the Graphviz software suite. dot-app enables the interchange of networks between Cytoscape and DOT-compatible applications so that users can benefit from the features of both. dot-app was first deployed to the Cytoscape App Store in August 2015, has since registered more than 1,200 downloads, and has been highly rated by more than 20 users.