publication . Article . Other literature type . 2016

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

Braxton Fitts; Ziran Zhang; Massoud Maher; Barry Demchak;
  • Published: 20 Oct 2016
  • Publisher: F1000 ( Faculty of 1000 Ltd)
Abstract
<ns4:p>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 Cytos...
Subjects
free text keywords: Bioinformatics, Medicine, R, Biology (General), QH301-705.5, Software Tool Article, Articles, Network, import, export, format conversion, attribute conversion, Cytoscape, GraphViz, DOT, Large networks, Computer science, Disk formatting, App store, Graph, Programming language, computer.software_genre, computer, Plug-in, Data visualization, business.industry, business, Graph Layout, Network topology, Neuroscience
Funded by
NIH| Core_Training
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2P41GM103504-06
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

1 Shannon P Markiel A Ozier O: Cytoscape: a software environment for integrated models of biomolecular interaction networks.Genome Res.2003;13(11):2498–504. 10.1101/gr.1239303 14597658 [OpenAIRE] [PubMed] [DOI]

2 Roughan M Tuke J: Unravelling graph-exchange file formats. arXiv preprint arXiv:1503.02781.2015 Reference Source [OpenAIRE]

3 Gansner ER North SC: An open graph visualization system and its applications to software engineering.Software Pract Exper.2000;30(11):1203–1233. 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.3.CO;2-E [DOI]

4 Fitts B Zhang Z Maher M: dot-app.ZENODO.2017 Data Source [OpenAIRE]

Abstract
<ns4:p>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 Cytos...
Subjects
free text keywords: Bioinformatics, Medicine, R, Biology (General), QH301-705.5, Software Tool Article, Articles, Network, import, export, format conversion, attribute conversion, Cytoscape, GraphViz, DOT, Large networks, Computer science, Disk formatting, App store, Graph, Programming language, computer.software_genre, computer, Plug-in, Data visualization, business.industry, business, Graph Layout, Network topology, Neuroscience
Funded by
NIH| Core_Training
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2P41GM103504-06
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

1 Shannon P Markiel A Ozier O: Cytoscape: a software environment for integrated models of biomolecular interaction networks.Genome Res.2003;13(11):2498–504. 10.1101/gr.1239303 14597658 [OpenAIRE] [PubMed] [DOI]

2 Roughan M Tuke J: Unravelling graph-exchange file formats. arXiv preprint arXiv:1503.02781.2015 Reference Source [OpenAIRE]

3 Gansner ER North SC: An open graph visualization system and its applications to software engineering.Software Pract Exper.2000;30(11):1203–1233. 10.1002/1097-024X(200009)30:11<1203::AID-SPE338>3.3.CO;2-E [DOI]

4 Fitts B Zhang Z Maher M: dot-app.ZENODO.2017 Data Source [OpenAIRE]

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publication . Article . Other literature type . 2016

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

Braxton Fitts; Ziran Zhang; Massoud Maher; Barry Demchak;