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BioPAX Cytoscape PlugIn
Version 0.3 of the Cytoscape BioPAX PlugIn is now available.
(requires Cytoscape v2.3 or greater)
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BioPAX PlugIn Features
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Enables Cytoscape users to load and visually render BioPAX files from the web or a local file system.
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Supports BioPAX Levels 1 and 2.
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User can click on any node and immediately view BioPAX details about that node. When possible, links are provided to external resources, such as UniProt, PubMed, Entrez Gene, AmiGo (Gene Ontology), and IHOP (Information Hyperlinked Over Proteins).
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Default visual style automatically maps BioPAX entity types to specific shapes. For example, physical entities, such as proteins are represented as circles, whereas interaction entities are represented as diamonds, etc.
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Distribution includes sample BioPAX documents, including sample files from Reactome, and Ecocyc.
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Verified to work with moderate size BioPAX files. For example, the PlugIn will parse a 504KB BioPAX document with 340 nodes and 470 edges in 700 ms.
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Includes new Simplified Visual Language support.
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Small download. Easy 1-step installation.
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Sample Screenshot
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[Click Image to Enlarge]
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Download
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Version 0.3 (requires Cytoscape v2.3 or greater) *
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* Note:
After the release of Cytoscape v2.3.1, a conflict between BioPAX Plugin v0.3 and the CytoscapeEditor.jar that shipped with Cytoscape was discovered. To resolve this conflict, replace Cytoscape-v2.3.1/plugins/CytoscapeEditor.jar with the following CytoscapeEditor.jar. In addition, Mac users also need to replace Cytoscape-v2.3.1/cytoscape-v2.3.1.app/Contents/Resources/Java/CytoscapeEditor.jar.
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Version 0.2 (requires Cytoscape v2.2)
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README File / Installation Instructions
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View the README.html included in the download distribution.
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The BioPAX project is funded in part by U.S. Department of Energy Workshop Grant #DE-FG02-04ER63931
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