Release 2.6 Use Cases / Overall Themes

Timeline

Release Date:

Release 2.6 Features

New Features

Title

Lead

Description

Status

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.

Peng

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

Ready for testing

Dynamic Filtering algorithm

Peng

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.

Testing

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)

Kei

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

Mike

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

Clean up old bugs

Everyone

Ongoing.

In memory session saving

Mike

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

Properties

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.

Allan

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

Scooter

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

Ready for testing

Load Network from URL improvements

Scooter

Enhance the Load Network from URL to not use temporary files

Ready for testing

Load Networks

Ben

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

Linkout from Attribute Browser

Kei

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 GeorgeWright)

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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