Release 2.6 Use Cases / Overall Themes


Release Date:

Release 2.6 Features

New Features





Cytoscape Themes.

Sarah and Alex

We think it would be useful to provide customized versions of Cytoscape for specific users. An example would be a biologist themed release that would include all plugins to support import/export of biological file formats.

Ready for testing

Filter UI redesign.


To construct complex filter with the combination of AND, OR, and NOT.

Ready for testing

Dynamic Filtering algorithm


develop an algorithm to apply filter with time complexity ~ lnN. N is the total number of nodes and edges.The intent for the changes to the filters UI is to allow dynamic selection of nodes and edges based sliders and other widgets in the filter. This isn't possible for 2.5 so we've pushed it to 2.6.


Refactor the Network Manager to support selection and operations on multiple networks.

Mike and Kei

It is often the case that users have hundreds of networks loaded at any given time. It would be useful to be able to perform operations (such as applying a layout) on more than one network at once. Also, we need to separate Network Panel's tree data model from GUI.

Ready for Testing

Web Service Client Manager and User Interface for Bio Web Services (Biomart/NCBI/KEGG)


Provide a simple interface to bio-database web services that will facilitate id mapping and attribute import in Cytoscape. This will address use cases 3 and 4 listed here.

RFC is ready. IntAct, NCBI and Biomart clients are ready for testing.

Modal Label Positioning


Provide an edit mode to Cytoscape that allows node labels to be moved simply by clicking on them and dragging.

Clean up old bugs



In memory session saving


Explore writing a session file without first writing tmp files. We should be able to do everything in memory. This will prevent many permission error bugs.

Ready for Testing


Mike and Sarah

We need global properties that are saved in the .cytoscape directory automatically, in addition to the cytoscape.props. Some use cases are: saving the last directory used, saving bookmarks stored by users.

Will not be part of 2.6, may be part of a maintenance release of 2.6

Workflow Panel.


A CytoPanel that presents a list of actions corresponding to the steps of the Nature Protocols workflow above. When the user clicks on an item in the list, the appropriate step in the workflow is initiated.

XGMML improvements


Rewrite the XGMML reader and writer to significantly reduce the transient memory use and improve performance.

Ready for testing

Load Network from URL improvements


Enhance the Load Network from URL to not use temporary files

Ready for testing

Load Networks


Update the existing Pathway Commons Plugin (which provides connectivity between and Cytoscape) to provide similar functionality as the cPath Plugin.

Linkout from Attribute Browser


Get Linkout and Linkout from Attribute Browser using the same code. Make sure that linkout works for any attribute, not just ID.

Ready for testing

Enlist non-core developers

Backlogs from 2.5

Move to 3.0

Testing Cytoscape 2.6

Cytoscape_2.6 (last edited 2009-06-02 19:10:02 by 142)

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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