Differences between revisions 28 and 37 (spanning 9 versions)

Cytoscape 3.0 (and beyond) Development Modules

Contents

Cytoscape 3.0 (and beyond) Development Modules
Re-architected 2.6 Features
New for 3.0
Usability/Management
Future target (Post 3.0)

Comments:

A status of "Incomplete" means that essentially no work has been done for this module in 3.0. Module size is a rough estimate of how much code or data is contained in that module. Module impact refers to how much a change in that module will impact other modules. Module impact is not meant to be a value judgment! It merely tries to communicate how many other modules have dependencies on it. Module leader helps organize, manage, contribute and delegate. Multiple interested people can contribute to a module. Once you’ve taken the lead – update the module definition and status on a weekly basis on the wiki.

Re-architected 2.6 Features

model

Description:	The core network and data table models used by everyone else.
3.0 Status:	The API and an implementation are largely complete.
Leading 3.0 work:	UCSD (Mike Smoot)
Interest:	Everyone
Who did the work in 2.x:	everyone
Module size:	Large
Module impact:	Large

Bundles	Developers	Status
model-api	Mike Smoot (UCSD)	Largely complete
model-impl	Mike Smoot (UCSD)	Largely complete

work

Description:	An API for defining and executing Tasks, configuring the Tasks, and supporting undo.
3.0 Status:	The API and implementation are largely complete. API documentation and tutorial for Tasks completed.
Leading 3.0 work:	Pasteur (Samad Lotia, Mathieu Michaud)
Interest:	UCSD (Mike Smoot)
Who did the work in 2.x:	(didn't exist prior to 3.0)
Module size:	Large
Module impact:	Large

Bundles	Developers	Status
work-api	Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD)	Largely complete
work-swing-impl	Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD)	Largely complete
work-spring-hack	Mike Smoot (UCSD)	Largely complete
work-tunable-props-impl	Mathieu Michaud (Pasteur)	???

logging

Description:	Both developer and user logging framework.
3.0 Status:	Largely complete. Tutorial completed.
Leading 3.0 work:	Pasteur (Samad Lotia)
Interest:	UCSD (Mike Smoot), ISB
Who did the work in 2.x:	UCSF, ISB
Module size:	Small
Module impact:	Medium

Bundles	Developers	Status
log-swing	Samad Lotia (Pasteur)	Completed.

io

Description:	APIs for importing and exporting data including networks, tables, sessions, and images.
3.0 Status:	The API is largely defined, but all implementations need to be refined.
Leading 3.0 work:	Unilever (Noel Ruddock)
Interest:	Toronto (Brian Turner), UCSD (Kei Ono), Pasteur (Samad Lotia), Piet Molenaar (AMC), Mike Smoot (UCSD)
Who did the work in 2.x:	everyone
Module size:	Large
Module impact:	Large

Bundles	Developers	Status
io-api	Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD)	Largely complete
io-impl	Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD), ???	halfway?
sbml	Noel Ruddock (Unilever)	Incomplete, just starting
psi-mi	Piet Molenaar (AMC Amsterdam)	Incomplete, just starting
biopax	Rex Dwyer, Arman Aksoy, Emek Demir, Ethan Cerami currently working to support BioPAX level 3 in 2.6 using paxtools (with a lite xml reader replacing Jena). Once this is done, the code can be moved to 3.0	Incomplete

view-model

Description:	An API that defines the visualization of a network (and later table), but doesn't actually do the rendering.
3.0 Status:	The API and implementation are largely complete.
Leading 3.0 work:	UCSD (Mike Smoot)
Interest:	Daniel Abel (ELTE), general interest from everyone
Who did the work in 2.x:	(didn't exist prior to 3.0)
Module size:	Medium
Module impact:	Large

Bundles	Developers	Status
viewmodel-api	Daniel Abel, Mike Smoot (UCSD)	Largely complete
viewmodel-impl	Daniel Abel, Mike Smoot (UCSD)	Largely complete

vizmap

Description:	An API that modifies a view-model based on attribute (data table) values.
3.0 Status:	The API is largely complete and the user interface implementation is nearing completion.
Leading 3.0 work:	UCSD (Kei Ono)
Interest:	Daniel Abel (ELTE)
Who did the work in 2.x:	(didn't exist prior to 3.0)
Module size:	Medium
Module impact:	Small

Bundles	Developers	Status
vizmap-api	Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD)	more than halfway
vizmap-impl	Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD)	more than halfway
vizmap-gui	Kei Ono (UCSD)	halfway

presentation

Description:	An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model.
3.0 Status:	The API has been sketched and an implementation is in place, but it needs a lot of refinement.
Leading 3.0 work:	UCSD (Mike Smoot, Kei Ono), Daniel Abel (ELTE)
Interest:
Who did the work in 2.x:	everyone
Module size:	Large
Module impact:	Medium

Bundles	Developers	Status
presentation-api	Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD)	halfway
ding-presentation-impl	Kei Ono (UCSD), Mike Smoot (UCSD)	halfway
graph-render	Mike Smoot (UCSD)	Largely complete
util-intr	Mike Smoot (UCSD)	Largely complete
spacial	Mike Smoot (UCSD)	Largely complete

attribute-presentation

Description:	An implementation that renders a data table.
3.0 Status:	Incomplete.
Leading 3.0 work:	???
Interest:	UCSD (Kei Ono)
Who did the work in 2.x:	UCSD (Kei Ono), others
Module size:	Small
Module impact:	Small

Bundles	Developers	Status
attribute-browser	???	Incomplete

editor

Description:	A user interface that allows users to add, delete, and change nodes and edges in a network.
3.0 Status:	Incomplete.
Leading 3.0 work:	Agilent (Allan Kuchinsky)
Interest:	Piet Molenaar (AMC)
Who did the work in 2.x:	Agilent
Module size:	Medium
Module impact:	Small

Bundles	Developers	Status
editor	Allan Kuchinsky (Agilent)	Incomplete

layout

Description:	An API and several implementations of layout algorithms that modify the view-model for a given network.
3.0 Status:	Incomplete.
Leading 3.0 work:	UCSF (Scooter Morris)
Interest:	Benno Schwikowski (Pasteur), Mike Smoot (UCSD), Allan Kuchinsky (Agilent), Alex Pico (UCSF)
Who did the work in 2.x:	UCSF, UCSD
Module size:	Large
Module impact:	Small

Bundles	Developers	Status
layout-api	Mike Smoot (UCSD)	Largely complete
layout-cytoscape-impl	Daniel Abel and Mike Smoot	Largely complete
layout-jgraph-impl	Daniel Abel and Mike Smoot	Largely complete
layout-prefuse-impl	Daniel Abel and Mike Smoot	Largely complete

search/filters

Description:	An API and user interface that allows a network to be searched and/or filtered.
3.0 Status:	~50% complete. API is complete, based on ESP code and Lucene v.2.4.1. UI design is also complete. The new UI is an integration of Filters, QuickFind and ESP UI and offers new features such as history and filtering out of search results. Current work is on implementing UI and testing various use cases.
Leading 3.0 work:	UCSD (Peng Wang), Maital Ashkenazi (Evogene)
Interest:	Allan Kuchinsky (Agilent), Mike Smoot (UCSD)
Who did the work in 2.x:	MSKCC, Maital Ashkenazi, UCSD
Module size:	Medium
Module impact:	Medium

Bundles	Developers	Status
quickfind	Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)	Incomplete
filters	Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)	Incomplete
ESP	Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)	Incomplete
search-API	Srinivas Vundavalli (GSOC)	Incomplete
search-UI	Srinivas Vundavalli (GSOC)	Incomplete

groups

Description:	An API and user interface that allows groups of nodes to be defined and captured as subnetworks.
3.0 Status:	Incomplete.
Leading 3.0 work:	UCSF (Scooter Morris)
Interest:	Alex Pico (UCSF), Allan Kuchinsky (UCSF)
Who did the work in 2.x:	UCSF
Module size:	Medium?
Module impact:	Medium

Bundles	Developers	Status
groups	???	Incomplete

merge

Description:	An API that provides for set operations on networks based on attributes of the networks.
3.0 Status:	Incomplete.
Leading 3.0 work:	David States (???)
Interest:	Kei Ono (UCSD)
Who did the work in 2.x:	UCSD (Kei Ono), GSOC
Module size:	Small
Module impact:	Small

Bundles	Developers	Status
merge	???	Incomplete, Jianjiong Gao (GSOC)

linkout

Description:	An API that allows objects in Cytoscape to be linked to web databases.
3.0 Status:	Incomplete.
Leading 3.0 work:	???
Interest:	Allan Kuchinsky (Agilent)
Who did the work in 2.x:	MSKCC (Doron Betel), Agilent (Allan Kuchinsky)
Module size:	Small
Module impact:	Small

Bundles	Developers	Status
linkout	Allan Kuchinsky (Agilent)	Incomplete

webservices

Description:	An API that provides a common interface for accessing web based interaction databases.
3.0 Status:	Some work has been done, but incomplete.
Leading 3.0 work:	Sarah Killcoyne (ISB)???
Interest:	UCSD (Kei Ono), Piet Molenaar (AMC)
Who did the work in 2.x:	MSKCC (Ethan Cerami), UCSD (Kei Ono)
Module size:	Small
Module impact:	Medium

Bundles	Developers	Status
webservices	Kei Ono (UCSD)	just proof-of-concept code
cpath2 - aka Pathway Commons plugin	???	Incomplete

swing-application

Description:	A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape").
3.0 Status:	About 75% complete (excluding core plugins).
Leading 3.0 work:	UCSD (Mike Smoot)
Interest:	Everyone
Who did the work in 2.x:	everyone
Module size:	Large
Module impact:	Large

Bundles	Developers	Status
application	Mike Smoot (UCSD)	more than halfway
session-api	Mike Smoot (UCSD)	only an initial interface
splash	Mike Smoot (UCSD)	largely complete

plugin-manager

Description:	A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles.
3.0 Status:	The user interface is largely finished, but still needs to be integrated with the swing application.
Leading 3.0 work:	UCSD (Peng Wang)
Interest:	Sarah Killcoyne (ISB)
Who did the work in 2.x:	ISB (Sarah Killcoyne), UCSD (Peng Wang)
Module size:	Large
Module impact:	Medium

Bundles	Developers	Status
ui2	Peng Wang (UCSD)	more than halfway
ui2-sdk	Peng Wang (UCSD)	more than halfway
ui2-sdk-scheduler	Peng Wang (UCSD)	more than halfway
Cytoscape 3 Plugin website	Peng Wang (UCSD)	incomplete

New for 3.0

command-line-application

Description:	A command-line application built from low-level cytoscape modules that can perform various tasks (e.g. load a networks, lay it out, and render it to an image file) without the need for a graphical user interface.
3.0 Status:	Partially completed.
Leading 3.0 work:	Pasteur (Mathieu Michaud)
Interest:	Mike Smoot (UCSD)
Who did the work in 2.x:	(didn't exist prior to 3.0)
Module size:	Medium
Module impact:	Medium

Bundles	Developers	Status
work-headless-impl	Mathieu Michaud (Pasteur)	Largely completed.
cmdline-application	Mathieu Michaud (Pasteur)	Largely completed.
cmdline-parser-impl	Mathieu Michaud (Pasteur)	Largely completed.

scripting

Description:	An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API.
3.0 Status:	Incomplete.
Leading 3.0 work:	???
Interest:	UCSD (Kei Ono), ISB (Sarah Killcoyne)
Who did the work in 2.x:	UCSF, UCSD
Module size:	Small?
Module impact:	Small

Bundles	Developers	Status
scripting?	???	Incomplete

web-application

Description:	A web-based version of Cytoscape.
3.0 Status:	Usable beta version complete and available as part of the beta.genemania.org website
Leading 3.0 work:	University of Toronto, Christian Lopes (GeneMANIA group, Bader Lab, Toronto).
Interest:	Sarah Killcoyne, Hector Rovira (ISB), DanielAbel, Piet Molenaar (AMC)
Who did the work in 2.x:	(didn't exist prior to 3.0)
Module size:	Large
Module impact:	Small

Usability/Management

qa/testing

Description:	The management and oversight of the development, planning, and execution of unit tests, functional tests, acceptance tests, performance tests, and general promotion of "quality."
3.0 Status:	Started May.2009
Leading 3.0 work:	Toronto (Farzana Kazi)
Interest:	George Wright (Toronto)
Who did the work in 2.x:	There are a few unit tests scattered about contributed by different groups, but no comprehensive strategy.
Module size:	Medium
Module impact:	Large

Task	Developers	Status
Test plan for 2.6.2	Farzana Kazi, George Wright	Test plan for Cytoscape 2.6.2 is complete. Once Cytoscape 3.0 is ready, we can use this test plan for measuring completeness of 3.0. See Cytoscape_3.0/Enhanced Test Plan

documentation

Description:	The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention.
3.0 Status:	Incomplete.
Leading 3.0 work:	???
Interest:
Who did the work in 2.x:	everyone
Module size:	Large
Module impact:	Large

usability

Description:	The evaluation and refinement of Cytoscape usability including usability testing and tracking.
3.0 Status:	Inactive.
Leading 3.0 work:	???
Interest:
Who did the work in 2.x:	Pasteur, ???
Module size:	Small
Module impact:	it depends

dev-process

Description:	The management and oversight of the development processes, build tools, release tools and processes for Cytoscape.
3.0 Status:	Ongoing.
Leading 3.0 work:	???
Interest:	Sarah Killcoyne (ISB), Brian Turner (UofT)
Who did the work in 2.x:	everyone
Module size:	Small
Module impact:	Large

architecture

Description:	The management and oversight of the overall Cytoscape architecture and how different modules interact with one another.
3.0 Status:	It exists, but is poorly documented.
Leading 3.0 work:	UCSD (Mike Smoot)
Interest:	Sarah Killcoyne (ISB)
Who did the work in 2.x:	everyone
Module size:	Small
Module impact:	Large

Future target (Post 3.0)

decorated-networks

Description:	A future project for providing enhanced visualizations of networks in cytoscape with other background and foreground graphics and text (e.g. cell location).
3.0 Status:	Two Google Summer of Code Project are ongoing
Leading 3.0 work:	UCSF (Alex Pico, Scooter Morris, Allan Kuchinsky) - ???
Interest:	Piet Molenaar (AMC)
Who did the work in 2.x:	UCSF, MSKCC, Agilent
Module size:	Large?
Module impact:	Medium

Bundles	Developers	Status
decorated-networks	???	Incomplete, UCSD (Kei. Proof-of-concept code only)

database-backend

Description:	A future project that will provide a relational (or other) database backend for Cytoscape.
3.0 Status:	Future project.
Leading 3.0 work:	???
Interest:	Scooter Morris (UCSF), Alex Pico (UCSF)
Who did the work in 2.x:	(didn't exist prior to 3.0)
Module size:	???
Module impact:	Small

Bundles	Developers	Status
database-backend	???	Incomplete

extended-cydatatable

Description:	A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities.
3.0 Status:	Future project.
Leading 3.0 work:	???
Interest:	Scooter Morris (UCSF)
Who did the work in 2.x:	(didn't exist prior to 3.0)
Module size:	???
Module impact:	Small

Bundles	Developers	Status
extended-cydatatable	???	Incomplete

Outdated_Cytoscape_3.0/DevelopmentModules (last edited 2011-02-24 15:35:42 by PietMolenaar)

-  ← Revision 28 as of 2009-06-12 11:48:28 →
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  Comment: Added Piet as interested in webapplication and decorated-networks modules
+  ← Revision 37 as of 2009-09-04 13:27:51 →
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  Comment:
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 <<TableOfContents(2)>>
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-||''Description:'' ||The core network and data table models used by everyone else.||

||''3.0 Status:'' ||The API and an implementation are largely complete.||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot)||

||''Interest:'' || Everyone ||

||''Who did the work in 2.x:'' ||everyone||

||''Module size:''||Large  ||

||''Module impact:''||Large  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/model-api/trunk|model-api]]||Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/model-impl/trunk|model-impl]]||Mike Smoot (UCSD)||Largely complete||
+||''Description:'' ||The core network and data table models used by everyone else. ||

||''3.0 Status:'' ||The API and an implementation are largely complete. ||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot) ||

||''Interest:'' ||Everyone ||

||''Who did the work in 2.x:'' ||everyone ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Large ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/model-api/trunk|model-api]] ||Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/model-impl/trunk|model-impl]] ||Mike Smoot (UCSD) ||Largely complete ||
 Line 24:
-||''Description:'' ||An API for defining and executing Tasks, configuring the Tasks, and supporting undo.||

||''3.0 Status:'' ||The API and implementation are largely complete.||

||''Leading 3.0 work:'' ||Pasteur (Samad Lotia, Mathieu Michaud)||

||''Interest:'' || UCSD (Mike Smoot) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)||

||''Module size:''||Large ||

||''Module impact:''||Large  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/work-api/trunk|work-api]]||Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/work-swing-impl/trunk|work-swing-impl]]||Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/work-spring-hack/trunk|work-spring-hack]]||Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/work-headless-impl/trunk|work-headless-impl]]||Samad Lotia (Pasteur)||just beginning||

||[[http://chianti.ucsd.edu/svn/core3/work-tunable-props-impl/trunk|work-tunable-props-impl]]||Mathieu Michaud (Pasteur)||???||
+||''Description:'' ||An API for defining and executing Tasks, configuring the Tasks, and supporting undo. ||

||''3.0 Status:'' ||The API and implementation are largely complete. API documentation and tutorial for Tasks completed. ||

||''Leading 3.0 work:'' ||Pasteur (Samad Lotia, Mathieu Michaud) ||

||''Interest:'' ||UCSD (Mike Smoot) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0) ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Large ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/work-api/trunk|work-api]] ||Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/work-swing-impl/trunk|work-swing-impl]] ||Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/work-spring-hack/trunk|work-spring-hack]] ||Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/work-tunable-props-impl/trunk|work-tunable-props-impl]] ||Mathieu Michaud (Pasteur) ||??? ||
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-||''Description:'' ||Both developer and user logging framework.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' ||Pasteur (Samad Lotia)||

||''Interest:'' || UCSD (Mike Smoot) ||

||''Who did the work in 2.x:'' ||UCSF, ISB||

||''Module size:''||Small  ||

||''Module impact:''||Medium  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/log-swing/trunk|log-swing]]||Samad Lotia (Pasteur)||In progress||
+||''Description:'' ||Both developer and user logging framework. ||

||''3.0 Status:'' || Largely complete. Tutorial completed. ||

||''Leading 3.0 work:'' ||Pasteur (Samad Lotia) ||

||''Interest:'' ||UCSD (Mike Smoot), ISB ||

||''Who did the work in 2.x:'' ||UCSF, ISB ||

||''Module size:'' ||Small ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/log-swing/trunk|log-swing]] ||Samad Lotia (Pasteur) ||Completed. ||
-Line 52:
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-||''Description:'' ||APIs for importing and exporting data including networks, tables, sessions, and images.||

||''3.0 Status:'' ||The API is largely defined, but all implementations need to be refined.||

||''Leading 3.0 work:'' || Unilever (Noel Ruddock)||

||''Interest:'' || Toronto (Brian Turner), UCSD (Kei Ono), Pasteur (Samad Lotia), Piet Molenaar (AMC), Mike Smoot (UCSD) ||

||''Who did the work in 2.x:'' ||everyone||

||''Module size:''||Large  ||

||''Module impact:''||Large  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/io-api/trunk|io-api]]||Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/io-impl/trunk|io-impl]]||Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD), ???||halfway?||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|sbml]]||Noel Ruddock (Unilever)||Incomplete, just starting||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|psi-mi]]||Piet Molenaar (AMC Amsterdam)||Incomplete, just starting||
+||''Description:'' ||APIs for importing and exporting data including networks, tables, sessions, and images. ||

||''3.0 Status:'' ||The API is largely defined, but all implementations need to be refined. ||

||''Leading 3.0 work:'' ||Unilever (Noel Ruddock) ||

||''Interest:'' ||Toronto (Brian Turner), UCSD (Kei Ono), Pasteur (Samad Lotia), Piet Molenaar (AMC), Mike Smoot (UCSD) ||

||''Who did the work in 2.x:'' ||everyone ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Large ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/io-api/trunk|io-api]] ||Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/io-impl/trunk|io-impl]] ||Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD), ??? ||halfway? ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|sbml]] ||Noel Ruddock (Unilever) ||Incomplete, just starting ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|psi-mi]] ||Piet Molenaar (AMC Amsterdam) ||Incomplete, just starting ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|biopax]] ||Rex Dwyer, Arman Aksoy, Emek Demir, Ethan Cerami currently working to support BioPAX level 3 in 2.6 using paxtools (with a lite xml reader replacing Jena). Once this is done, the code can be moved to 3.0 ||Incomplete ||
-Line 67:
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-||''Description:'' ||An API that '''''defines''''' the visualization of a network (and later table), but doesn't actually do the rendering.||

||''3.0 Status:'' ||The API and implementation are largely complete.||
+||''Description:'' ||An API that '''''defines''''' the visualization of a network (and later table), but doesn't actually do the rendering. ||

||''3.0 Status:'' ||The API and implementation are largely complete. ||
-Line 70:
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-||''Interest:'' || Daniel Abel (ELTE), general interest from everyone ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)||

||''Module size:''||Medium ||

||''Module impact:''||Large ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/viewmodel-api/trunk|viewmodel-api]]||Daniel Abel, Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/viewmodel-impl/trunk|viewmodel-impl]]||Daniel Abel, Mike Smoot (UCSD)||Largely complete||
+||''Interest:'' ||Daniel Abel (ELTE), general interest from everyone ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0) ||

||''Module size:'' ||Medium ||

||''Module impact:'' ||Large ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/viewmodel-api/trunk|viewmodel-api]] ||Daniel Abel, Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/viewmodel-impl/trunk|viewmodel-impl]] ||Daniel Abel, Mike Smoot (UCSD) ||Largely complete ||
-Line 80:
+Line 87:
-||''Description:'' ||An API that modifies a view-model based on attribute (data table) values.||

||''3.0 Status:'' ||The API is largely complete and the user interface implementation is nearing completion.||

||''Leading 3.0 work:'' ||UCSD (Kei Ono)||

||''Interest:'' || Daniel Abel (ELTE) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)||

||''Module size:''||Medium ||

||''Module impact:''||Small ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/vizmap-api/trunk|vizmap-api]]||Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD)||more than halfway||

||[[http://chianti.ucsd.edu/svn/core3/vizmap-impl/trunk|vizmap-impl]]||Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD)||more than halfway||

||[[http://chianti.ucsd.edu/svn/core3/vizmap-gui/trunk|vizmap-gui]]||Kei Ono (UCSD)||halfway||
+||''Description:'' ||An API that modifies a view-model based on attribute (data table) values. ||

||''3.0 Status:'' ||The API is largely complete and the user interface implementation is nearing completion. ||

||''Leading 3.0 work:'' ||UCSD (Kei Ono) ||

||''Interest:'' ||Daniel Abel (ELTE) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0) ||

||''Module size:'' ||Medium ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/vizmap-api/trunk|vizmap-api]] ||Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD) ||more than halfway ||

||[[http://chianti.ucsd.edu/svn/core3/vizmap-impl/trunk|vizmap-impl]] ||Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD) ||more than halfway ||

||[[http://chianti.ucsd.edu/svn/core3/vizmap-gui/trunk|vizmap-gui]] ||Kei Ono (UCSD) ||halfway ||
-Line 94:
+Line 103:
-||''Description:'' ||An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model.||

||''3.0 Status:'' ||The API has been sketched and an implementation is in place, but it needs a lot of refinement.||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot, Kei Ono), Daniel Abel (ELTE)||
+||''Description:'' ||An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model. ||

||''3.0 Status:'' ||The API has been sketched and an implementation is in place, but it needs a lot of refinement. ||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot, Kei Ono), Daniel Abel (ELTE) ||
-Line 98:
+Line 107:
-||''Who did the work in 2.x:'' ||everyone||

||''Module size:''||Large ||

||''Module impact:''||Medium ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/presentation-api/trunk|presentation-api]]||Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD)||halfway||

||[[http://chianti.ucsd.edu/svn/core3/ding-presentation-impl/trunk|ding-presentation-impl]]||Kei Ono (UCSD), Mike Smoot (UCSD)||halfway||

||[[http://chianti.ucsd.edu/svn/core3/graph-render/trunk|graph-render]]||Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/util-intr/trunk|util-intr]]||Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/spacial/trunk|spacial]]||Mike Smoot (UCSD)||Largely complete||
+||''Who did the work in 2.x:'' ||everyone ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/presentation-api/trunk|presentation-api]] ||Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD) ||halfway ||

||[[http://chianti.ucsd.edu/svn/core3/ding-presentation-impl/trunk|ding-presentation-impl]] ||Kei Ono (UCSD), Mike Smoot (UCSD) ||halfway ||

||[[http://chianti.ucsd.edu/svn/core3/graph-render/trunk|graph-render]] ||Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/util-intr/trunk|util-intr]] ||Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/spacial/trunk|spacial]] ||Mike Smoot (UCSD) ||Largely complete ||
-Line 110:
+Line 121:
-||''Description:'' ||An implementation that renders a data table.||

||''3.0 Status:'' ||Incomplete.  ||

||''Leading 3.0 work:'' ||???||

||''Interest:'' || UCSD (Kei Ono) ||

||''Who did the work in 2.x:'' ||UCSD (Kei Ono), others||

||''Module size:''||Small ||

||''Module impact:''||Small ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|attribute-browser]]||???||Incomplete||
+||''Description:'' ||An implementation that renders a data table. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||??? ||

||''Interest:'' ||UCSD (Kei Ono) ||

||''Who did the work in 2.x:'' ||UCSD (Kei Ono), others ||

||''Module size:'' ||Small ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|attribute-browser]] ||??? ||Incomplete ||
-Line 122:
+Line 135:
-||''Description:'' ||A user interface that allows users to add, delete, and change nodes and edges in a network.||

||''3.0 Status:''  ||Incomplete.||

||''Leading 3.0 work:'' || Agilent (Allan Kuchinsky) ||

||''Interest:'' || Piet Molenaar (AMC) ||

||''Who did the work in 2.x:'' ||Agilent||

||''Module size:''||Medium ||

||''Module impact:''||Small ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|editor]]||Allan Kuchinsky (Agilent)||Incomplete||
+||''Description:'' ||A user interface that allows users to add, delete, and change nodes and edges in a network. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||Agilent (Allan Kuchinsky) ||

||''Interest:'' ||Piet Molenaar (AMC) ||

||''Who did the work in 2.x:'' ||Agilent ||

||''Module size:'' ||Medium ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|editor]] ||Allan Kuchinsky (Agilent) ||Incomplete ||
-Line 134:
+Line 149:
-||''Description:'' ||An API and several implementations of layout algorithms that modify the view-model for a given network.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' ||UCSF (Scooter Morris)||

||''Interest:'' || Benno Schwikowski (Pasteur), Mike Smoot (UCSD), Allan Kuchinsky (Agilent), Alex Pico (UCSF) ||

||''Who did the work in 2.x:'' ||UCSF, UCSD||

||''Module size:''||Large ||

||''Module impact:''||Small ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/core3/layout/trunk|layout]]||Mike Smoot (UCSD)||Largely complete||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|automatic-layout]]||???||Incomplete||
+||''Description:'' ||An API and several implementations of layout algorithms that modify the view-model for a given network. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||UCSF (Scooter Morris) ||

||''Interest:'' ||Benno Schwikowski (Pasteur), Mike Smoot (UCSD), Allan Kuchinsky (Agilent), Alex Pico (UCSF) ||

||''Who did the work in 2.x:'' ||UCSF, UCSD ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/layout-api/trunk|layout-api]] ||Mike Smoot (UCSD) ||Largely complete ||

||[[http://chianti.ucsd.edu/svn/core3/layout-cytoscape-impl/trunk|layout-cytoscape-impl]] ||Daniel Abel and Mike Smoot||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/layout-jgraph-impl/trunk|layout-jgraph-impl]] ||Daniel Abel and Mike Smoot||Largely complete||

||[[http://chianti.ucsd.edu/svn/core3/layout-prefuse-impl/trunk|layout-prefuse-impl]] ||Daniel Abel and Mike Smoot||Largely complete||
-Line 147:
+Line 165:
-||''Description:'' ||An API and user interface that allows a network to be searched and/or filtered.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' || UCSD (Peng Wang), Maital Ashkenazi (Evogene) ||

||''Interest:'' || Allan Kuchinsky (Agilent), Mike Smoot (UCSD)||

||''Who did the work in 2.x:'' ||MSKCC, Maital Ashkenazi, UCSD||

||''Module size:''||Medium  ||

||''Module impact:''||Medium  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|quickfind]]||Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)||Incomplete||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|filters]]||Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)||Incomplete||
+||''Description:'' ||An API and user interface that allows a network to be searched and/or filtered. ||

||''3.0 Status:'' || ~50% complete. API is complete, based on ESP code and Lucene v.2.4.1. UI design is also complete. The new UI is an integration of Filters, QuickFind and ESP UI and offers new features such as history and filtering out of search results. Current work is on implementing UI and testing various use cases. ||

||''Leading 3.0 work:'' ||UCSD (Peng Wang), Maital Ashkenazi (Evogene) ||

||''Interest:'' ||Allan Kuchinsky (Agilent), Mike Smoot (UCSD) ||

||''Who did the work in 2.x:'' ||MSKCC, Maital Ashkenazi, UCSD ||

||''Module size:'' ||Medium ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|quickfind]] ||Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD) ||Incomplete ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|filters]] ||Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD) ||Incomplete ||

||[[http://chianti.ucsd.edu/svn/csplugins/trunk/soc/maital/EnhancedSearch/|ESP]] ||Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD) ||Incomplete ||

||search-API ||Srinivas Vundavalli (GSOC) ||Incomplete ||

||search-UI ||Srinivas Vundavalli (GSOC) ||Incomplete ||
-Line 160:
+Line 183:
-||''Description:'' ||An API and user interface that allows groups of nodes to be defined and captured as subnetworks.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' ||UCSF (Scooter Morris)||

||''Interest:'' || Alex Pico (UCSF), Allan Kuchinsky (UCSF) ||

||''Who did the work in 2.x:'' ||UCSF||

||''Module size:''||Medium?  ||

||''Module impact:''||Medium  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||groups||???||Incomplete||
+||''Description:'' ||An API and user interface that allows groups of nodes to be defined and captured as subnetworks. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||UCSF (Scooter Morris) ||

||''Interest:'' ||Alex Pico (UCSF), Allan Kuchinsky (UCSF) ||

||''Who did the work in 2.x:'' ||UCSF ||

||''Module size:'' ||Medium? ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||groups ||??? ||Incomplete ||
-Line 172:
+Line 197:
-||''Description:'' ||An API that provides for set operations on networks based on attributes of the networks.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' ||David States (???)||

||''Interest:'' || Kei Ono (UCSD) ||

||''Who did the work in 2.x:'' ||UCSD (Kei Ono), GSOC||

||''Module size:''||Small  ||

||''Module impact:''||Small  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]]||???||Incomplete, Jianjiong Gao (GSOC)||
+||''Description:'' ||An API that provides for set operations on networks based on attributes of the networks. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||David States (???) ||

||''Interest:'' ||Kei Ono (UCSD) ||

||''Who did the work in 2.x:'' ||UCSD (Kei Ono), GSOC ||

||''Module size:'' ||Small ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]] ||??? ||Incomplete, Jianjiong Gao (GSOC) ||
-Line 184:
+Line 211:
-||''Description:'' ||An API that allows objects in Cytoscape to be linked to web databases.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' ||???||

||''Interest:'' || Allan Kuchinsky (Agilent) ||

||''Who did the work in 2.x:'' ||MSKCC (Doron Betel), Agilent (Allan Kuchinsky)||

||''Module size:''||Small  ||

||''Module impact:''||Small  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]]||Allan Kuchinsky (Agilent)||Incomplete||
+||''Description:'' ||An API that allows objects in Cytoscape to be linked to web databases. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||??? ||

||''Interest:'' ||Allan Kuchinsky (Agilent) ||

||''Who did the work in 2.x:'' ||MSKCC (Doron Betel), Agilent (Allan Kuchinsky) ||

||''Module size:'' ||Small ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|linkout]] ||Allan Kuchinsky (Agilent) ||Incomplete ||
-Line 196:
+Line 225:
-||''Description:'' ||An API that provides a common interface for accessing web based interaction databases.||

||''3.0 Status:'' ||Some work has been done, but incomplete.||

||''Leading 3.0 work:'' ||???||

||''Interest:'' || UCSD (Kei Ono), Piet Molenaar (AMC) ||

||''Who did the work in 2.x:'' ||MSKCC (Ethan Cerami), UCSD (Kei Ono)||

||''Module size:''||Small  ||

||''Module impact:''||Medium  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|webservices]]||Kei Ono (UCSD)||just proof-of-concept code||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|biopax]]||???||Incomplete||
+||''Description:'' ||An API that provides a common interface for accessing web based interaction databases. ||

||''3.0 Status:'' ||Some work has been done, but incomplete. ||

||''Leading 3.0 work:'' ||Sarah Killcoyne (ISB)??? ||

||''Interest:'' ||UCSD (Kei Ono), Piet Molenaar (AMC) ||

||''Who did the work in 2.x:'' ||MSKCC (Ethan Cerami), UCSD (Kei Ono) ||

||''Module size:'' ||Small ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|webservices]] ||Kei Ono (UCSD) ||just proof-of-concept code ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|cpath2]] - aka Pathway Commons plugin ||??? ||Incomplete ||
-Line 209:
+Line 240:
-||''Description:'' ||A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape").||

||''3.0 Status:'' ||About 75% complete (excluding core plugins).||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot)||

||''Interest:'' || Everyone ||

||''Who did the work in 2.x:'' ||everyone||

||''Module size:''||Large  ||

||''Module impact:''||Large  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|application]]||Mike Smoot (UCSD)||more than halfway||

||[[http://chianti.ucsd.edu/svn/core3/session-api/trunk|session-api]]||Mike Smoot (UCSD)||only an initial interface||

||[[http://chianti.ucsd.edu/svn/core3/splash/trunk|splash]]||Mike Smoot (UCSD)||largely complete||
+||''Description:'' ||A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape"). ||

||''3.0 Status:'' ||About 75% complete (excluding core plugins). ||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot) ||

||''Interest:'' ||Everyone ||

||''Who did the work in 2.x:'' ||everyone ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Large ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|application]] ||Mike Smoot (UCSD) ||more than halfway ||

||[[http://chianti.ucsd.edu/svn/core3/session-api/trunk|session-api]] ||Mike Smoot (UCSD) ||only an initial interface ||

||[[http://chianti.ucsd.edu/svn/core3/splash/trunk|splash]] ||Mike Smoot (UCSD) ||largely complete ||
-Line 223:
+Line 256:
-||''Description:'' ||A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles.||

||''3.0 Status:'' ||The user interface is largely finished, but still needs to be integrated with the swing application.||

||''Leading 3.0 work:'' ||UCSD (Peng Wang)||

||''Interest:'' || Sarah Killcoyne (ISB) ||

||''Who did the work in 2.x:'' ||ISB (Sarah Killcoyne), UCSD (Peng Wang)||

||''Module size:''||Large  ||

||''Module impact:''||Medium  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||[[http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/cyprovision|ui2]]||Peng Wang (UCSD)||more than halfway||

||[[http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/cyprovision|ui2-sdk]]||Peng Wang (UCSD)||more than halfway||

||[[http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/cyprovision|ui2-sdk-scheduler]]||Peng Wang (UCSD)||more than halfway||

||Cytoscape 3 Plugin website||Peng Wang (UCSD)||incomplete||
+||''Description:'' ||A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles. ||

||''3.0 Status:'' ||The user interface is largely finished, but still needs to be integrated with the swing application. ||

||''Leading 3.0 work:'' ||UCSD (Peng Wang) ||

||''Interest:'' ||Sarah Killcoyne (ISB) ||

||''Who did the work in 2.x:'' ||ISB (Sarah Killcoyne), UCSD (Peng Wang) ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/cyprovision|ui2]] ||Peng Wang (UCSD) ||more than halfway ||

||[[http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/cyprovision|ui2-sdk]] ||Peng Wang (UCSD) ||more than halfway ||

||[[http://chianti.ucsd.edu/svn/csplugins/trunk/ucsd/pwang/cyprovision|ui2-sdk-scheduler]] ||Peng Wang (UCSD) ||more than halfway ||

||Cytoscape 3 Plugin website ||Peng Wang (UCSD) ||incomplete ||
-Line 238:
+Line 273:
-Line 240:
+Line 274:
-||''Description:'' ||A command-line application built from low-level cytoscape modules that can perform various tasks (e.g. load a networks, lay it out, and render it to an image file) without the need for a graphical user interface.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' || Pasteur (Mathieu Michaud) ||

||''Interest:'' || Mike Smoot (UCSD) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)||

||''Module size:''||Medium ||

||''Module impact:''||Medium ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||work.headless (TBD) ||???||Incomplete||
+||''Description:'' ||A command-line application built from low-level cytoscape modules that can perform various tasks (e.g. load a networks, lay it out, and render it to an image file) without the need for a graphical user interface. ||

||''3.0 Status:'' ||Partially completed. ||

||''Leading 3.0 work:'' ||Pasteur (Mathieu Michaud) ||

||''Interest:'' ||Mike Smoot (UCSD) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0) ||

||''Module size:'' ||Medium ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||[[http://chianti.ucsd.edu/svn/core3/work-headless-impl/trunk|work-headless-impl]] ||Mathieu Michaud (Pasteur) ||Largely completed. ||

||cmdline-application ||Mathieu Michaud (Pasteur) ||Largely completed. ||

||cmdline-parser-impl ||Mathieu Michaud (Pasteur) ||Largely completed. ||
-Line 252:
+Line 290:
-||''Description:'' ||An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' || ??? ||

||''Interest:'' || UCSD (Kei Ono) ||

||''Who did the work in 2.x:'' ||UCSF, UCSD||

||''Module size:''||Small? ||

||''Module impact:''||Small ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||scripting?||???||Incomplete||
+||''Description:'' ||An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||??? ||

||''Interest:'' ||UCSD (Kei Ono), ISB (Sarah Killcoyne) ||

||''Who did the work in 2.x:'' ||UCSF, UCSD ||

||''Module size:'' ||Small? ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||scripting? ||??? ||Incomplete ||
-Line 264:
+Line 304:
-||''Description:'' ||A web-based version of Cytoscape.||

||''3.0 Status:'' ||Usable beta version complete and available as part of the beta.genemania.org website||

||''Leading 3.0 work:'' ||University of Toronto, Christian Lopes (GeneMANIA group, Bader Lab, Toronto).||

||''Interest:'' ||Sarah Killcoyne, Hector Rovira (ISB), DanielAbel, Piet Molenaar (AMC)||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)||

||''Module size:''||Large ||

||''Module impact:''||Small ||
+||''Description:'' ||A web-based version of Cytoscape. ||

||''3.0 Status:'' ||Usable beta version complete and available as part of the beta.genemania.org website ||

||''Leading 3.0 work:'' ||University of Toronto, Christian Lopes (GeneMANIA group, Bader Lab, Toronto). ||

||''Interest:'' ||Sarah Killcoyne, Hector Rovira (ISB), DanielAbel, Piet Molenaar (AMC) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0) ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Small ||
-Line 273:
+Line 314:
-Line 275:
+Line 315:
-||''Description:'' ||The management and oversight of the development, planning, and execution of unit tests, functional tests, acceptance tests, performance tests, and general promotion of "quality."||

||''3.0 Status:'' ||Started May.2009||

||''Leading 3.0 work:'' ||Toronto (Farzana Kazi)||

||''Interest:'' || George Wright (Toronto) ||

||''Who did the work in 2.x:'' ||There are a few unit tests scattered about contributed by different groups, but no comprehensive strategy.||

||''Module size:''||Medium  ||

||''Module impact:''||Large ||



||'''Task'''||'''Developers'''||'''Status'''||

||Test plan for 2.6.2||Farzana, George|| Developing a test plan for Cytoscape 2.6.2 that can then be used for measuring completeness of 3.0. Work expected to be complete over the summer 2009. See [[Cytoscape_2.6/Test Plan - 2.6]]||
+||''Description:'' ||The management and oversight of the development, planning, and execution of unit tests, functional tests, acceptance tests, performance tests, and general promotion of "quality." ||

||''3.0 Status:'' ||Started May.2009 ||

||''Leading 3.0 work:'' ||Toronto (Farzana Kazi) ||

||''Interest:'' ||George Wright (Toronto) ||

||''Who did the work in 2.x:'' ||There are a few unit tests scattered about contributed by different groups, but no comprehensive strategy. ||

||''Module size:'' ||Medium ||

||''Module impact:'' ||Large ||





||'''Task''' ||'''Developers''' ||'''Status''' ||

||Test plan for 2.6.2 ||Farzana Kazi, George Wright||Test plan for Cytoscape 2.6.2 is complete. Once Cytoscape 3.0 is ready, we can use this test plan for measuring completeness of 3.0. See [[Cytoscape_3.0/Enhanced Test Plan]] ||
-Line 287:
+Line 329:
-||''Description:'' ||The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention.||

||''3.0 Status:'' ||Incomplete.||

||''Leading 3.0 work:'' ||???||
+||''Description:'' ||The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention. ||

||''3.0 Status:'' ||Incomplete. ||

||''Leading 3.0 work:'' ||??? ||
-Line 291:
+Line 333:
-||''Who did the work in 2.x:'' ||everyone||

||''Module size:''||Large  ||

||''Module impact:''||Large  ||
+||''Who did the work in 2.x:'' ||everyone ||

||''Module size:'' ||Large ||

||''Module impact:'' ||Large ||
-Line 296:
+Line 339:
-||''Description:'' ||The evaluation and refinement of Cytoscape usability including usability testing and tracking.||

||''3.0 Status:'' ||Inactive.||

||''Leading 3.0 work:'' ||???||
+||''Description:'' ||The evaluation and refinement of Cytoscape usability including usability testing and tracking. ||

||''3.0 Status:'' ||Inactive. ||

||''Leading 3.0 work:'' ||??? ||
-Line 300:
+Line 343:
-||''Who did the work in 2.x:''  ||Pasteur, ???||

||''Module size:''||Small  ||

||''Module impact:''||it depends  ||
+||''Who did the work in 2.x:'' ||Pasteur, ??? ||

||''Module size:'' ||Small ||

||''Module impact:'' ||it depends ||
-Line 305:
+Line 349:
-||''Description:'' ||The management and oversight of the development processes, build tools, release tools and processes for Cytoscape.||

||''3.0 Status:'' ||Ongoing.||

||''Leading 3.0 work:'' || ??? ||

||''Interest:'' || Sarah Killcoyne (ISB), Brian Turner (UofT) ||

||''Who did the work in 2.x:'' ||everyone||

||''Module size:''||Small  ||

||''Module impact:''||Large  ||
+||''Description:'' ||The management and oversight of the development processes, build tools, release tools and processes for Cytoscape. ||

||''3.0 Status:'' ||Ongoing. ||

||''Leading 3.0 work:'' ||??? ||

||''Interest:'' ||Sarah Killcoyne (ISB), Brian Turner (UofT) ||

||''Who did the work in 2.x:'' ||everyone ||

||''Module size:'' ||Small ||

||''Module impact:'' ||Large ||
-Line 314:
+Line 359:
-||''Description:'' ||The management and oversight of the overall Cytoscape architecture and how different modules interact with one another.||

||''3.0 Status:'' ||It exists, but is poorly documented.||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot)||

||''Interest:'' || ||

||''Who did the work in 2.x:'' ||everyone||

||''Module size:''||Small  ||

||''Module impact:''||Large  ||
+||''Description:'' ||The management and oversight of the overall Cytoscape architecture and how different modules interact with one another. ||

||''3.0 Status:'' ||It exists, but is poorly documented. ||

||''Leading 3.0 work:'' ||UCSD (Mike Smoot) ||

||''Interest:'' ||Sarah Killcoyne (ISB)||

||''Who did the work in 2.x:'' ||everyone ||

||''Module size:'' ||Small ||

||''Module impact:'' ||Large ||
-Line 323:
+Line 369:
-Line 325:
+Line 370:
-||''Description:'' ||A future project for providing enhanced visualizations of networks in cytoscape with other background and foreground graphics and text (e.g. cell location).||

||''3.0 Status:'' ||Two Google Summer of Code Project are ongoing||

||''Leading 3.0 work:'' ||UCSF (Alex Pico, Scooter Morris, Allan Kuchinsky) - ???||

||''Interest:'' || Piet Molenaar (AMC)||

||''Who did the work in 2.x:'' ||UCSF, MSKCC, Agilent||

||''Module size:''||Large?  ||

||''Module impact:''||Medium  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||decorated-networks||???||Incomplete, UCSD (Kei. Proof-of-concept code only)||
+||''Description:'' ||A future project for providing enhanced visualizations of networks in cytoscape with other background and foreground graphics and text (e.g. cell location). ||

||''3.0 Status:'' ||Two Google Summer of Code Project are ongoing ||

||''Leading 3.0 work:'' ||UCSF (Alex Pico, Scooter Morris, Allan Kuchinsky) - ??? ||

||''Interest:'' ||Piet Molenaar (AMC) ||

||''Who did the work in 2.x:'' ||UCSF, MSKCC, Agilent ||

||''Module size:'' ||Large? ||

||''Module impact:'' ||Medium ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||decorated-networks ||??? ||Incomplete, UCSD (Kei. Proof-of-concept code only) ||
-Line 337:
+Line 384:
-||''Description:'' ||A future project that will provide a relational (or other) database backend for Cytoscape.||

||''3.0 Status:'' ||Future project.||

||''Leading 3.0 work:'' ||???||

||''Interest:'' || Scooter Morris (UCSF), Alex Pico (UCSF) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)||

||''Module size:''||??? ||

||''Module impact:''||Small ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||database-backend||???||Incomplete||
+||''Description:'' ||A future project that will provide a relational (or other) database backend for Cytoscape. ||

||''3.0 Status:'' ||Future project. ||

||''Leading 3.0 work:'' ||??? ||

||''Interest:'' ||Scooter Morris (UCSF), Alex Pico (UCSF) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0) ||

||''Module size:'' ||??? ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||database-backend ||??? ||Incomplete ||
-Line 349:
+Line 398:
-||''Description:'' ||A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities.||

||''3.0 Status:'' ||Future project.||

||''Leading 3.0 work:'' ||???||

||''Interest:'' || Scooter Morris (UCSF) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)||

||''Module size:''||???  ||

||''Module impact:''||Small  ||



||'''Bundles'''||'''Developers'''||'''Status'''||

||extended-cydatatable||???||Incomplete||
+||''Description:'' ||A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities. ||

||''3.0 Status:'' ||Future project. ||

||''Leading 3.0 work:'' ||??? ||

||''Interest:'' ||Scooter Morris (UCSF) ||

||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0) ||

||''Module size:'' ||??? ||

||''Module impact:'' ||Small ||





||'''Bundles''' ||'''Developers''' ||'''Status''' ||

||extended-cydatatable ||??? ||Incomplete ||

Diff for "Outdated_Cytoscape_3.0/DevelopmentModules"