Differences between revisions 20 and 23 (spanning 3 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.

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.
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-headless-impl	Samad Lotia (Pasteur)	just beginning
work-tunable-props-impl	Mathieu Michaud (Pasteur)	???

logging

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
log-swing	Samad Lotia (Pasteur)	In progress

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
psi-mi	Piet Molenaar (AMC Amsterdam)	Incomplete, just starting

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	Mike Smoot (UCSD)	Largely complete
automatic-layout	???	Incomplete

search/filters

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
quickfind	Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)	Incomplete
filters	Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)	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
merge	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:	???
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
biopax	???	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:	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

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)
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
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, 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

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:
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:
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 20 as of 2009-06-11 16:35:33 →
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  Editor: cache
  Comment:
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+||''Interest:'' || Everyone ||
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-||''Leading 3.0 work:'' ||Pasteur (???)||

||''Interest:'' || UCSD (???) ||
+||''Leading 3.0 work:'' ||Pasteur (Samad Lotia, Mathieu Michaud)||

||''Interest:'' || UCSD (Mike Smoot) ||
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-||''3.0 Status:'' ||In progress.||
+||''3.0 Status:'' ||Incomplete.||
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-||''Interest:'' || ||
+||''Interest:'' || UCSD (Mike Smoot) ||
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-||''Interest:'' || Toronto (Brian Turner), UCSD (Kei Ono), Pasteur (Samad Lotia) ||
+||''Interest:'' || Toronto (Brian Turner), UCSD (Kei Ono), Pasteur (Samad Lotia), Piet Molenaar (AMC), Mike Smoot (UCSD) ||
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-||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|sbml]]||???||Incomplete||
+||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|sbml]]||Noel Ruddock (Unilever)||Incomplete||
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-||''Interest:'' || Daniel Abel ||
+||''Interest:'' || Daniel Abel (ELTE), general interest from everyone ||
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+||''Interest:'' || Daniel Abel (ELTE) ||
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-||''Leading 3.0 work:'' ||UCSD (Mike Smoot, Kei Ono)||

||''Interest:'' || Daniel Abel ||
+||''Leading 3.0 work:'' ||UCSD (Mike Smoot, Kei Ono), Daniel Abel (ELTE)||

||''Interest:'' || ||
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-||''Interest:'' || ||

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

||''Module size:''||Small  ||

||''Module impact:''||Small  ||
+||''Interest:'' || UCSD (Kei Ono) ||

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

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

||''Module impact:''||Small ||
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-||''Leading 3.0 work:'' ||??? ||

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

||''Interest:'' || Piet Molenaar (AMC) ||
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-||''Module size:''||Medium  ||

||''Module impact:''||Small  ||
+||''Module size:''||Medium ||

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

||''Interest:'' || Pasteur (Benno Schwikowski) ||
+||''Leading 3.0 work:'' ||UCSF (Scooter Morris)||

||''Interest:'' || Benno Schwikowski (Pasteur), Mike Smoot (UCSD), Allan Kuchinsky (Agilent), Alex Pico (UCSF) ||
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||''Module impact:''||Small  ||
+||''Module size:''||Large ||

||''Module impact:''||Small ||
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||''Interest:'' || ||
+||''Leading 3.0 work:'' || UCSD (Peng Wang), Maital Ashkenazi (Evogene) ||

||''Interest:'' || Allan Kuchinsky (Agilent), Mike Smoot (UCSD)||
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-||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|filters.old]]||Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)||Incomplete||
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-||''Leading 3.0 work:'' ||UCSF (Alex Pico, Scooter Morris, Allan Kuchinsky)||

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

||''Interest:'' || Alex Pico (UCSF), Allan Kuchinsky (UCSF) ||
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-||''Leading 3.0 work:'' ||David States||

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

||''Who did the work in 2.x:'' ||UCSD||
+||''Leading 3.0 work:'' ||David States (???)||

||''Interest:'' || Kei Ono (UCSD) ||

||''Who did the work in 2.x:'' ||UCSD (Kei Ono), GSOC||
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-||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]]||???||Incomplete, GSOC project||
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-||''Interest:'' || ||

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

||''Who did the work in 2.x:'' ||MSKCC (Doron Betel), Agilent (Allan Kuchinsky)||
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-||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]]||???||Incomplete||
+||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]]||Allan Kuchinsky (Agilent)||Incomplete||
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-||''Leading 3.0 work:'' ||UCSD||

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

||''Who did the work in 2.x:'' ||MSKCC, Toronto, UCSD||
+||''Leading 3.0 work:'' ||???||

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

||''Who did the work in 2.x:'' ||MSKCC (Ethan Cerami), UCSD (Kei Ono)||
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-== 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:'' ||UCSD(Kei, proof-of-concept code only)||

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

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

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

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



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

||scripting||???||Incomplete||
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-||''Leading 3.0 work:'' ||UCSD||

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

||''Interest:'' || Everyone ||
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+Line 222:
-== 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:'' ||Incomplete.||

||''Leading 3.0 work:'' || Pasteur (???) ||

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

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

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

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



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

||scripting||???||Incomplete||
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-||''Leading 3.0 work:'' ||UCSD||

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

||''Who did the work in 2.x:'' ||ISB, UCSD||
+||''Leading 3.0 work:'' ||UCSD (Peng Wang)||

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

||''Who did the work in 2.x:'' ||ISB (Sarah Killcoyne), UCSD (Peng Wang)||
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-= 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:'' ||UofT, Farzana Kazi, George Wright (Bader lab)||

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

||''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]]||



== 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:'' ||ISB, Toronto, UCSD||

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

||''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||

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

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

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

||''Module impact:''||Large  ||
+||Cytoscape 3 Plugin website||Peng Wang (UCSD)||incomplete||
-Line 313:
+Line 239:
-== 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:'' || ||

||''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)||
+== 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:'' ||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||



== 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) ||

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

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

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



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

||scripting?||???||Incomplete||
-Line 334:
+Line 272:
+= 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, 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]]||



== 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:'' || ||

||''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:'' || ||

||''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 338:
+Line 340:
-||''Interest:'' || ||

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

||''Module size:''||???  ||

||''Module impact:''||Small  ||
+||''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 ||
-Line 350:
+Line 352:
-||''Interest:'' || ||
+||''Interest:'' || Scooter Morris (UCSF) ||

Diff for "Outdated_Cytoscape_3.0/DevelopmentModules"