NEW! Cytoscape 2.6.2
This is a bug-fix release that should work with all 2.6.x plugins. There are no API changes.
Some issues that have been addressed in this release include:
- Fixed the webstart on Mac OS X problem.
- Fixed Linkout for Linux when no default browser is set.
- Fixed bugs: 1865, 1939, 1940, 1927, 1858, 1957, 1917, among others.
- Improved handling of metanodes.
- Improvements in the attribute browser that so that new line characters can now be specified.
- Improved all Cytoscape layouts to support graph partitioning, selected only, and so that configuration parameters are saved.
- Fixed various documentation issues.
- Fixed URL loading issues related to file type.
- Many other minor improvements.
Cytoscape 2.6.1
This is a minor bug-fix release that should work with all 2.6.0 plugins.
There are no API changes, however we have added a new centralized logging facility. See Help->Error Console to see Cytoscape's startup messages and any warnings or errors that occur during operation.
Some Bugs that have been fixed include:
- Topology filter performance
- XGMML loading consistency
- Mac usability issues
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 2.5.2
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
[PubMed entry].
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.
[Abstract] [PDF] [PubMed entry].
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).
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.
