F656F4C4d01 - Systems Biology - Cytoscape - Jens H ll d...

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Unformatted text preview: Systems Biology - Cytoscape - Jens H ll d 12/4/2009 Hollunder Academic Year 2009-2010 1 Cytoscape: Analyzing and Cytoscape: Analyzing and Vi li i N t k D t Visualizing Network Data http://www.cytoscape.org/ What is Cytoscape? Free available (open source) bioinformatics • Free available (open source) bioinformatics software platform software platform • Visualization and analysis of networks • Integration of supported data, e.g. annotations and gene expression • Functionality could be expanded by using plug-ins Systems Biology - Cytoscape - Jens H ll d 12/4/2009 Hollunder Academic Year 2009-2010 2 Features Supports a lot of standard network and • Supports a lot of standard network and annotation file formats including: annotation file formats including: – SIF (Simple Interaction Format) Features Supports a lot of standard network and • Supports a lot of standard network and annotation file formats including: annotation file formats including: – SIF (Simple Interaction Format) – GML, XGMML Systems Biology - Cytoscape - Jens H ll d 12/4/2009 Hollunder Academic Year 2009-2010 3 Features Supports a lot of standard network and • Supports a lot of standard network and annotation file formats including: annotation file formats including: – SIF (Simple Interaction Format) – GML, XGMML , – BioPAX Features Supports a lot of standard network and • Supports a lot of standard network and annotation file formats including: annotation file formats including: – SIF (Simple Interaction Format) – GML, XGMML, – BioPAX, PSI-MI, SBML, – OBO Systems Biology - Cytoscape - Jens H ll d 12/4/2009 Hollunder Academic Year 2009-2010 4 Features Supports a lot of standard network and • Supports a lot of standard network and annotation file formats including: – SIF (Simple Interaction Format) – GML, XGMML, – BioPAX PS MI SBML – BioPAX, PSI-MI, SBML, – OBO, and Gene Association – Delimited text files and MS Excel™ Workbook – expression profiles or GO annotations – …. Interoperability Supports import/export standard file formats • Supports import/export standard file formats Systems Biology - Cytoscape - Jens H ll d 12/4/2009 Hollunder Academic Year 2009-2010 5 Web Service Clients Cytoscape works as a web service clien • Cytoscape works as a web service client Cytoscape can directly connect to the externa • Cytoscape can directly connect to the external public databases • Pathway Commons, • IntAct BioMar • BioMart • NCBI Entrez Gene • … Web Service Clients Cytoscape works as a web service clien • Cytoscape works as a web service client Cytoscape can directly connect to the externa • Cytoscape can directly connect to the external public databases we developed a Cytoscape plug-in...
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F656F4C4d01 - Systems Biology - Cytoscape - Jens H ll d...

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