Name

Lead Group

Time Required

Status

Remaining Development Time

Layout Manager / Broker

UCSF - Scooter

checked in/awaiting feedback

testing

Groups (formerly known as metanodes)

UCSF, Agilent

Completed API and two client plugins (namedSelectionPlugin, metanodePlugin2)

testing

Hyperedges

Agilent

1-2 weeks

finalizing documentation, testing

Document Event Handling (preliminary work to event handling refactoring, write Doclets)

Everyone

["VizMapUI"] Redesign

UCSD - Kei

Need to fix icon generator problems

testing and compatibility test

tuning and testing. Swing-unit tests are required.

Plugin Website

UCSD - Peng

10 weeks

Test site is at http://cytoscape.org/plugins25/index.php

0 day

Automatic Plugin Download

ISB - Sarah

PluginManager API and dialog code in place, writing documentation

testing

Create cytoscape-helpdesk

UCSD - Peng

2 weeks

FAQ is in progress

Peformance (speed + memory) profiling

UCSD - Mike, AMC - Piet

1 week

Framework complete, just need to add a few more events

1 week

Pathway Commons Connectivity

MSKCC, Gary

ETA, May 7.

Plugin and webservices API in progress.

1.5 weeks

["Filters UI Redesign"]

MSKCC - Ethan, UCSD - Mike, Peng

7 weeks

Implementation is in progress

1.5 weeks

Library Reduction / Cleanup

ISB - Sarah

1 week

ongoing

finished

Testing

AMC - Piet, Pasteur - Tero

1 week

Undo Manager

AMC - Piet, UCSD - Mike

Checked in/awaiting feedback

testing

Interactive Layout (Bubble, Snap-To)

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

1-2 weeks

bubble-router mostly implemented, nearing internal release to core developers

Plan to release as plugin with 2.5

["Layers / Annotation / UI for custom nodes"]

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

TBD (requires further study of renderer)

some initial functionality implemented, and utilized in bubble router prototype

Planning for 2.6

Papers

Everyone

Bug Fixing

Everyone

Remove Deprecation Warnings

Everyone

ongoing

ongoing

Name

Lead Group

Time Required

Status

Tutorials

Unassigned

Usability Assessment

Pasteur, ISB - Sarah

ongoing

ongoing

Web Services / Database Connectivity Guidelines

ISB - Sarah, UCSF - Alex

RFC started, discussions ongoing

ongoing - Planning for 2.6

Linkout from Attribute Browser

UCSD - Kei

1-2 weeks

Prototype is already there, but need to integrate it with Linkout plugin.

Custom Node / Edge Graphics (MIMS)

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

Cytoscape Class Cleanup

MSKCC - Ethan

Combining Attributes / Formulas

MSKCC - Ethan, UCSF - Scooter, Alex

GINY Refactoring

UCSD - Mike

Properties / XML Config

UCSD,UCSF - Scooter

1 month (? Depends on the goal)

Planning

CyAttributes Name Clashes

MSKCC - Ethan

Lower priority; will be completed if there is time, after Pathway Commons and Filters.