Cytoscape

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2.6.0 Release Notes »

About Cytoscape

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
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Download Cytoscape

Download Version 2.6.0 (Requires Java SE 5 or Java SE 6)

2.6.0 Release Notes »

Online Tutorials

Get Started with the expanded Cytoscape online tutorials. Eight tutorials describe Cytoscape from basic operation to detailed plugin operation.

Manual

HTML format or PDF format, explains all basic features of Cytoscape. Get Acrobat reader

Developers

Roadmap Javadoc API Wiki Graph INterface librarY (GINY) Download Source from SVN

New! Cytoscape 2.6.0

Cytoscape 2.6 Screenshot
(Updated 4/11/2008) New features include:
  • Web Service Client Manager
    • Seamless access to Pathway Commons, IntAct, and NCBI Entrez Gene.
    • Synonym import from BioMart.
  • Cytoscape Themes
  • Dynamic Filters
  • Network Manager supports multiple network selection
  • Label Positioning has been improved
  • Session saving occurs in memory
  • XGMML loading/saving optimized
  • Linkout integrated with attribute browser
  • Extra sample Visual Styles using new visual properties
  • Many, many bug fixes!
Cytoscape 2.6.0 release notes

Cytoscape 2.5.2

This is a bug-fix release that addresses issues related to XGMML loading and parsing old vizmap.props files. Enjoy!

Cytoscape 2.5.1

A point release to address a variety of bugs in the 2.5.0 release.

Cytoscape 2.5.0

Cytoscape 2.5 Screenshot
(Updated 7/23/2007) New features include:
  • New VizMapper User Interface
    • More intuitive
    • Continuous mapping editors
    • Visual editor for default view
    • Visual mapping browser
    • Improved visual legend generator
    • Utilities to generate discrete values
  • New Features for Visual Style
    • Transparency (opactiy) support
    • Continuous edge width
    • Color visual property is separated from Arrow and Edge
  • New Filter User Interface
    • Intuitive widgets for basic filters
    • Suggested search values with indexing
    • Options to save in session or globally.
  • Plugin Manager and New Plugin Website
    • Install/Update/Delete plugins from within Cytoscape
    • Search for version compatible plugins from any host site
    • Display list of installed plugins
  • Layout customization
  • Undo and Redo
  • Group API for plugin developers
  • Node stacking
  • Tested on both Java SE 5 and 6
  • Many, many bug fixes!

Cytoscape Retreat 2007!

Amsterdam by night
Now in Europe! November 6th - 9th
Including a public symposium on November 8th, with a formidable list of confirmed speakers among them
  • Leroy Hood
  • Peter Sorger
  • Ewan Birney
Hosted by the Human Genetics Department of the Academic Medical Center in the vibrant historic city of Amsterdam.

Cytoscape 2.4.1

No new features, but several bugs have been fixed.

Cytoscape 2.4.0

Cytoscape 2.4.0 Screenshot
(Updated 1/16/2007)
New features include:
  • Publication quality image generation.
    • Node label position adjustment.
    • Automatic Visual Legend generator.
    • Node position fine-tuning by arrow keys.
    • The ability to override selected VizMap settings.
  • Quick Find plugin.
  • New icons for a cleaner user interface.
  • Consolidated network import capabilities.
    • Import network from remote data sources (through http or ftp).
    • Default support for the following file formats: SBML, BioPAX, PSI-MI, Delimited text, Excel.
  • New Ontology Server.
    • Native support for OBO format ontology files.
    • Ability to visualize the ontology tree as a network (DAG).
    • Full support for Gene Association files.
  • Support for Java SE 5
  • Many, many bug fixes!
See the Release Notes for more detail.

Publications about Cytoscape

Melissa S Cline, Michael Smoot, Ethan Cerami, Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas, Iliana Avila-Campilo, Michael Creech, Benjamin Gross, Kristina Hanspers, Ruth Isserlin, Ryan Kelley, Sarah Killcoyne, Samad Lotia, Steven Maere, John Morris, Keiichiro Ono, Vuk Pavlovic, Alexander R Pico, Aditya Vailaya, Peng-Liang Wang, Annette Adler, Bruce R Conklin, Leroy Hood, Martin Kuiper, Chris Sander, Ilya Schmulevich, Benno Schwikowski, Guy J Warner, Trey Ideker & Gary D Bader

Integration of biological networks and gene expression data using Cytoscape

Nature Protocols 2, 2366 - 2382 (2007) Published online: 27 September 2007 | doi:10.1038/nprot.2007.324

[PubMed entry].
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Genome Research 2003 Nov; 13(11):2498-504

[Abstract] [PDF] [PubMed entry].

Updated! (July 24 2007) Research using Cytoscape

As of July 2007, 281 publications are citing Shannon et al. (2003).

[Link to Publications Page]


Note: If you have a publication which makes use of Cytoscape, please let us know by sending an email to the cytoscape-discuss mailing list.

Past news articles are available here.

Getting Help:

Need help getting started with Cytoscape? Email our help-desk mailing list.

Cytoscape Announcements:

Cytoscape software engineer, Pasteur Institute, Paris (France).  April 23, 2008
  • The Systems Biology Group at the Pasteur Institute in Paris (France) has one-year vacancy for a software engineer. In collaboration with a number of groups in the United States, we are developing Cytoscape, the most popular open-source software platform for visualization and analysis of interaction networks. The person we are looking for will [cont.]

Save the date: Cytoscape retreat July 16-19, 2008 - Toronto.  April 16, 2008
  • On 16th – 19th July 2008 we will be hosting the 6th Annual Cytoscape Retreat at the Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada. [link] This year’s meeting is particularly exciting since it is the first time [cont.]

JavaScriptEngine Plugin v0.01.  April 15, 2008
  • Hi. For JavaScript programmers, I've created another scripting engine for Cytoscape. JavaScriptEngine Plugin 0.01 is also a technology preview for future version of Cytoscape. This plugin is based on Rhino 1.7.1: [link] and BSF 2.4.0, so you can use this in both Java 5 and 6. You can [cont.]

View All Announcements

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Cytoscape Community:

Cytoscape currently supports three mailing lists, all of which are hosted at Google Groups:

  • cytoscape-announce: Low-volume mailing list used to accounce new developments in Cytoscape.
    Subscribe | Browse Archives

  • cytoscape-helpdesk: Open forum for getting Cytoscape help. Geared towards new users.
    Subscribe | Browse Archives

  • cytoscape-discuss: Open forum for discussing Cytoscape, asking questions, suggesting new features, and developing plugins.
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Please join one of our mailing lists and get involved!

The Cytoscape project is an ongoing collaboration between:


 ISB Institute for Systems Biology

UCSD University of California at San Diego

MSKCC Memorial Sloan-Kettering Cancer Center
  IP Institut Pasteur

Agilent Agilent Technologies

UCSF University of California at San Francisco