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

(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

(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!

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-helpdesk: Subscribe | Browse Archives

Cytoscape Announcements:

Random Network Plugin Beta Release. August 13, 2008

Hello everyone, We are very excited to release the Beta version of the Random Network Plugin, a Google Summer of Code Project. Our plugin can be used for three main tasks: (1) Creating random networks according to three main models (erdos-renyi, watts-strogatz, barabasi-albert). (2) Create a degree(in/out) preserved randomization of an existing networks. [cont.]

Cytoscape programming job. July 14, 2008

Hi Everyone, We're hiring a full-time Cytoscape developer here at UCSD. Here is the job posting: [link] Please contact me off list if you have any questions! thanks, Mike [cont.]

CCMB/NCIBI MiMI plugin 3.0 release. June 17, 2008

The CCMB/NCIBI MiMI plugin 3.0 was released on June 16 2008 to Cytoscape using the latest version of mimiR2/geneR2 and pubmed_08n databases.
You can download MiMI plugin 3.0 from here: [link]
MiMI plugin 3.0 has the following improvements:
1. Faster performance due to the use of pre-computed tables for gene [cont.]

View All Announcements

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.
Subscribe | Browse Archives

Please join one of our mailing lists and get involved!