Cytoscape 2.7

Release 2.7 Use Cases / Overall Themes


Release 2.7 Features

New Features





Nested Networks


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


Several new edge types between solid and dashed have been added.

Ready for testing

Newlines and list editing in attribute browser


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


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


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


This allows access to any PSICQUIC compliant database.

Ready for testing



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

Test Cases - Cytoscape 2.7

Release notes

Subject: Cytoscape 2.7 is now available!

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

Cytoscape 2.7.0 improvements over previous versions include: 

Exciting new node shapes and edge line types - see
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

Cytoscape_2.7 (last edited 2010-03-18 16:26:58 by GaryBader)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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