Cytoscape Wiki
Cytoscape 2.7
Release 2.7 Use Cases / Overall Themes
- Get ready for NCRR Site Visit
- Quality improvements
- Targeted new features
Timeline
- Review of core API changes - Done: Feb.11.2010 - core API changes accepted after review/revision
- Testing to start by Farzana week of Feb.8. (need a stable test release for this)
- 2.7 beta1: Released ~Feb.10, now in testing.
Release 2.7 Features
New Features
Title |
Lead |
Description |
Status |
UCSD |
A node may now have a reference to another Network, which allows us to capture the relationships between networks in networks themselves. This feature includes a new file format (NNF) for nested network I/O and direct nested network editing via the Editor and Right-click menu. A Visual Property has been added to provide control of the visualization of the nested network. |
Ready for testing |
|
New Edge Types |
UCSD |
Several new edge types between solid and dashed have been added. |
Ready for testing |
Newlines and list editing in attribute browser |
UCSD |
The attribute browser has been updated to allow newline characters to be added by pressing the "Enter" key. List editing is now also enabled. |
Ready for testing |
Automatic label wrap |
UCSD |
A new visual property has been added that sets the width of a label. Any label extending beyond this width will be automatically wrapped. |
Ready for testing |
Arrow color optionally locked to edge color |
UCSD |
Arrow color may now be bound to the edge color by checking a box in the Dependencies pane of the Default Appearance Browser in the VizMapper, which avoids the necessity of creating separate-yet-identical mappings for edge, source, and target arrows. |
Ready for testing |
PSICQUIC Web Service plugin |
UCSD |
This allows access to any PSICQUIC compliant database. |
Ready for testing |
Scooter |
Addition of a mechanism to the core to provide inter-plugin communication |
Ready for testing |
|
BioPAX Level 3 support |
Toronto/Pathway Commons |
|
Ready for testing |
Release tasks
- Review core API changes
- Testing
- Create review of new features for testing
- Update the manual
Test Cases - Cytoscape 2.7
Release notes
Subject: Cytoscape 2.7 is now available! Message: Hi Everyone, The Cytoscape team is proud to announce the release of Cytoscape version 2.7.0! Cytoscape is an open-source software platform for visualizing interaction networks and integrating these interactions with other state data. You can download version 2.7.0 at http://cytoscape.org/ Cytoscape 2.7.0 improvements over previous versions include: Exciting new node shapes and edge line types - see http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual#Visual_Styles Ability to define and visualize nested networks. You can use this to view a network inside of a node, for example, if you want to define a hierarchy of network modules Improvements to web services, including access to IntAct and other interaction databases via the PSICQUIC service. BioMart and NCBI webservices now come with Cytoscape. Support for importing pathways in BioPAX Level 3 format Improved layouts for very large networks Many bug fixes For developers: plugins can now communicate with each other and advertise themselves as tasks via the CyCommand API Best regards, The Cytoscape Team http://cytoscape.org