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Cytoscape Online Tutorials

See our most up-to-date tutorials on OpenTutorials.

Older Tutorials

To get you started with Cytoscape: Getting Started Guide

The Cytoscape Online Tutorials from cytoscape.org have been moved here and updated for use with version 2.4.

• Basic Tutorials

  • Getting Started, Filters & Editor, Fetching External Data, Web Services Clients, Expression Analysis

• Advanced Tutorials

  • Literature Searching, Gene Ontology Annotation, Modules and Complexes, and Web Services

A Cytoscape tutorial series of lectures, videos, and exercises can be found at http://www.csc.fi/english/research/sciences/bioscience/Courses_and_events/cytoscape/index_html. Note that the videos require RealPlayer to view.

Presentations and Lecture Slides

Please feel free to use these lecture slides for your own presentations about Cytoscape.

• Print this Cytoscape Handout for your lectures

• CytoscapeAndR2_16_4_09.ppt A presentation on Cytoscape in general and a specific plugin R2 (by Piet Molenaar, partly based on slides by Tero Aittokallio)

• 2008 Systems Biology Conference Demos and Case Studies

• ISMB 2005 Tutorial

• BMES 2005 Tutorial

• Data Integration with Cytoscape at EMBL-EBI Biological Networks: Reconstruction, Analysis, and Modelling (May 5 & 6 2009)

  • Use Mondrian Cytoscape Web Start as a demonstration

  • LaTeX file, Makefile, included EPS files, and lecture notes as TeX comments

    • Requires beamer to be installed

    • EPS diagrams made with OmniGraffle

• Cytoscape 2.x Developers Tutorial

• Clusters and Groups Presentation

• 2010 Cytoscape Retreat User Tutorial

• EmblHeidelbergCytoscapeCourseSept2010

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