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dot-app: a {Graphviz}-{Cytoscape} conversion plug-in

Submitted by karopka on Tue, 2016/12/13 - 09:52
Titledot-app: a {Graphviz}-{Cytoscape} conversion plug-in
Publication TypeJournal Article
Year of Publication2016
AuthorsFitts, B, Zhang, Z, Maher, M, Demchak, B
JournalF1000Research
Volume5
Pagination2543
Keywordsattribute conversion, Cytoscape, Data visualization, DOT, export, format conversion, GraphViz, import, Network
Abstract

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, neato, smyrna, 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 offer all of the styling options that DOT-based applications (particularly GraphViz) do. dot-app enables the interchange of networks between Cytoscape and DOT-based 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.

DOI10.12688/f1000research.9751.1
PubMed ID27853520
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