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||Groups (formerly known as metanodes ||UCSF, Agilent || || Completed API and two client plugins (namedSelectionPlugin, metanodePlugin2) ||
||Hyperedges ||Agilent ||1-2 weeks || finalizing documentation, testing || 		||Groups (formerly known as metanodes ||UCSF, Agilent || ||Completed API and two client plugins (namedSelectionPlugin, metanodePlugin2) ||
||Hyperedges ||Agilent ||1-2 weeks ||finalizing documentation, testing ||
Line 17: Line 17:
||["VizMapUI"] Redesign ||UCSD - Kei || Alpha release in March || Building mockups and cleaning backend code ||
||Plugin Website / Automatic plugin download ||UCSD - Peng, ISB - Sarah ||10 weeks ||Planning/Design of website  Manager in place awaiting feedback, bug fixing||
||Linkout from Attribute Browser ||UCSD - Kei || 1-2 weeks ||Prototype is already there, but need to integrate it with Linkout plugin. ||
||Create cytoscape-helpdesk ||UCSD - Peng ||2 weeks || || 		||["VizMapUI"] Redesign ||UCSD - Kei ||Alpha release in March ||Building mockups and cleaning backend code ||
||Plugin Website / Automatic plugin download ||UCSD - Peng, ISB - Sarah ||10 weeks ||Planning/Design of website Manager in place awaiting feedback, bug fixing ||
||Linkout from Attribute Browser ||UCSD - Kei ||1-2 weeks ||Prototype is already there, but need to integrate it with Linkout plugin. ||
||Create cytoscape-helpdesk ||UCSD - Peng ||2 weeks ||FAQ is in progress ||
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||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.||
||Pathway Commons Connectivity ||MSKCC, Gary || TBD based on scope/design meeting 2/15 || RFC is in progress. ||
||Filters ||MSKCC - Ethan, UCSD - Mike || || Pending teleconference on Tuesday, March 26, 2007||
||Library Reduction / Cleanup ||ISB - Sarah ||1 week||ongoing ||
||Web Services / Database Connectivity Guidelines ||ISB - Sarah, UCSF - Alex ||2 weeks (more depending on goals)||ongong ||
||Usability Assessment ||Pasteur, ISB - Sarah ||ongoing||ongoing || 		||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. ||
||Pathway Commons Connectivity ||MSKCC, Gary ||TBD based on scope/design meeting 2/15 ||RFC is in progress. ||
||Filters ||MSKCC - Ethan, UCSD - Mike, Peng || ||RFC is in progress ||
||Library Reduction / Cleanup ||ISB - Sarah ||1 week ||ongoing ||
||Web Services / Database Connectivity Guidelines ||ISB - Sarah, UCSF - Alex ||2 weeks (more depending on goals) ||ongong ||
||Usability Assessment ||Pasteur, ISB - Sarah ||ongoing ||ongoing ||
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||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 ||
||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 || 		||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 ||
||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 ||

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

checked in/awaiting feedback

Groups (formerly known as metanodes

UCSF, Agilent

Completed API and two client plugins (namedSelectionPlugin, metanodePlugin2)

Hyperedges

Agilent

1-2 weeks

finalizing documentation, testing

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

Everyone

["VizMapUI"] Redesign

UCSD - Kei

Alpha release in March

Building mockups and cleaning backend code

Plugin Website / Automatic plugin download

UCSD - Peng, ISB - Sarah

10 weeks

Planning/Design of website Manager in place awaiting feedback, bug fixing

Linkout from Attribute Browser

UCSD - Kei

1-2 weeks

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

Create cytoscape-helpdesk

UCSD - Peng

2 weeks

FAQ is in progress

Peformance (speed + memory) profiling

UCSD - Mike, AMC - Piet

3 weeks

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.

Pathway Commons Connectivity

MSKCC, Gary

TBD based on scope/design meeting 2/15

RFC is in progress.

Filters

MSKCC - Ethan, UCSD - Mike, Peng

RFC is in progress

Library Reduction / Cleanup

ISB - Sarah

1 week

ongoing

Web Services / Database Connectivity Guidelines

ISB - Sarah, UCSF - Alex

2 weeks (more depending on goals)

ongong

Usability Assessment

Pasteur, ISB - Sarah

ongoing

ongoing

Testing

AMC - Piet, Pasteur - Tero

Undo Manager

AMC - Piet, UCSD - Mike

4 weeks

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

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

Papers

Everyone

Tutorials

Unassigned

Bug Fixing

Everyone

Remove Deprecation Warnings

Everyone

ongoing

ongoing

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

Cytoscape Class Cleanup

MSKCC - Ethan

Combining Attributes / Formulas

MSKCC - Ethan, UCSF - Scooter, Alex

Cytoscape_2.5 (last edited 2009-02-12 01:03:34 by localhost)

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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