TableOfContents

Release 2.5 Use Cases / Overall Themes

  1. Pathway / Annnotation
  2. Usability
  3. Navigation / Find

Timeline

Target Release Date: June 1, 2007

Release 2.5 Features

TODO

Name

Lead Group

Time Required

Status

Layout Manager / Broker

UCSF - Scooter

Groups (formerly known as metanodes

UCSF, Agilent

Hyperedges

Aglient

Document Event Handling (write Doclets)

Everyone (Mike Creech, Allan K, Ben Gross

Remove Deprecation Warnings

Everyone

ongoing

ongoing

Vizmap UI Redesign

UCSD - Kei

Plugin Website / Automatic plugin download

UCSD - Peng, ISB - Sarah

Linkout from Attribute Browser

UCSD

Create cytoscape-helpdesk

UCSD - Peng

Peformance (speed + memory) profiling

UCSD, AMC - Piet

GINY Refactoring

UCSD - Mike

Properties / XML Config

UCSD,UCSD - Scooter

Cytoscape Class Cleanup

MSKCC - Ethan

CyAttributes Name Clashes

MSKCC - Ethan

Pathway Commons Connectivity

MSKCC, Gary

Filters

MSKCC - Ethan, UCSD - Mike

Combining Attributes / Formulas

MSKCC - Ethan, UCSF - Scooter, Alex

Library Reduction / Cleanup

ISB - Sarah

Web Services / Database Connectivity Guidelines

ISB - Sarah, UCSF - Alex

Usability Assessment

Pasteur, ISB - Sarah

Testing

AMC - Piet, Pasteur - Tero

Undo Manager

AMC - Piet, UCSD - Peng

Interactive Layout (Bubble, Snap-To)

UCSF - Alex, Agilent - Allan K, MSKCC - Ben

Layers / Annotation / UI for cutsom nodes

UCSF - Alex, Agilent - Allan K, MSKCC - Ben

Papers

Everyone

Tutorials

Unassigned

Bug Fixing

Everyone

Completed

Name

Lead Group

Time Required

Status

Postponed

Name

Lead Group

Time Required

Status

Custom Node / Edge Graphics (MIMS)

UCSF - Alex, Agilent - Allan K, MSKCC - Ben

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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