Cytoscape Wiki|
Size: 636
Comment:
|
Size: 3808
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 9: | Line 9: |
| 2.7 beta1: End of February? |
* 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. |
| Line 16: | Line 18: |
|
||'''Embedded Networks''' ||UCSD || ||Ready for testing || ||'''New Edge Types''' ||UCSD || ||Ready for testing || |
||'''[[RFC_Nested_Networks|Nested Networks]]'''||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 [[http://code.google.com/p/psicquic/|PSICQUIC]] compliant database. ||Ready for testing || |
| Line 19: | Line 25: |
| ||'''BioPAX Level 3 support''' ||Toronto/Pathway Commons || ||Ready for testing || | |
| Line 20: | Line 27: |
|
= Testing Cytoscape 2.7 = * [[/Test Plan - 2.7|Test Plan - 2.7]] |
== Release tasks == * Review core API changes * Testing * Create review of new features for testing * Update the manual = Test Cases - Cytoscape 2.7 = * [[/Test Plan - 2.7 | Test cases related to Nested Networks]] * [[Cytoscape_2.7/New_Test_Cases| Test cases for new features in 2.7]] * [[/Core Plugins Test Cases| Core plugins_2.7]] * [[/UI Test Cases|Cytoscape Layout and User Interface 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 another 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 Support 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 |
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 another 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 Support 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