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

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          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.

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          Author and article information

          Journal
          F1000Res
          F1000Res
          F1000Research
          F1000Research
          F1000Research (London, UK )
          2046-1402
          20 October 2016
          2016
          : 5
          Affiliations
          [1 ]Department of Computer Science and Engineering, UC San Diego, San Diego, USA
          [2 ]Department of Health Sciences, UC San Diego, San Diego, USA
          [1 ]European Molecular Biology Laboratory (EMBL) Australia Group, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
          [1 ]Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany
          University of California, San Diego, USA
          [1 ]Institute of Genomics, CEA (French Alternative Energies and Atomic Energy Commission), Evry, France
          University of California, San Diego, USA
          Author notes

          Competing interests: No competing interests were disclosed.

          BF, ZZ, and MM were involved in writing the article. BF, ZZ, and BD were involved in revising the draft manuscript and have agreed on the final content. BF, ZZ, and MM were involved in designing and implementing dot-app. BD is the principal investigator for this dot-app project.

          Competing interests: No competing interests were disclosed.

          Competing interests: No competing interests were disclosed.

          Competing interests: No competing interests were disclosed.

          Competing interests: No competing interests were disclosed.

          Competing interests: No competing interests were disclosed.

          Article
          10.12688/f1000research.9751.1
          5105883
          Copyright: © 2016 Fitts B et al.

          This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

          Product
          Funding
          Funded by: National Institutes of Health
          Award ID: P41 GM103504
          This material is based upon work supported by the National Institutes of Health under Grant P41 GM103504. The grant is assigned to Dr. Trey Ideker at the University of California, San Diego (UCSD). All work was performed at UCSD.
          The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
          Categories
          Software Tool Article
          Articles
          Bioinformatics

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