New!Cytoscape 2.6.1
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
- 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
Cytoscape 2.5.1
Cytoscape 2.5.0
- 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
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].
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
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.