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dot-app: a Graphviz-Cytoscape conversion plug-in.

Braxton Fitts1, Ziran Zhang1, Massoud Maher1

  • 1Department of Computer Science and Engineering, UC San Diego, San Diego, USA.

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|July 28, 2017
PubMed
Summary
This summary is machine-generated.

dot-app facilitates seamless data exchange between Cytoscape and Graphviz DOT format applications. This integration allows users to leverage advanced network analysis in Cytoscape and superior graph styling in Graphviz.

Keywords:
CytoscapeDOTGraphVizNetworkattribute conversiondata visualizationexportformat conversionimport

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Network Science

Background:

  • Cytoscape is a popular platform for biological network analysis.
  • Graphviz (using DOT language) excels in graph layout and styling.
  • Limited interoperability exists between these tools, hindering combined usage.

Purpose of the Study:

  • To introduce dot-app, a Cytoscape 3 application.
  • To enable import and export of Graphviz DOT files within Cytoscape.
  • To bridge the gap between network analysis and visualization capabilities.

Main Methods:

  • Development of a Cytoscape 3 application (dot-app).
  • Implementation of functionalities for importing and exporting DOT files.
  • Testing compatibility with various DOT-compatible software.

Main Results:

  • dot-app successfully enables bidirectional file transfer between Cytoscape and DOT applications.
  • Users can now combine Cytoscape's analytical power with Graphviz's styling options.
  • The app has seen significant adoption since its 2015 release.

Conclusions:

  • dot-app enhances Cytoscape's utility by integrating DOT file compatibility.
  • It facilitates a more comprehensive approach to network visualization and analysis.
  • The application provides a valuable solution for researchers working with diverse network tools.