Differences between revisions 13 and 15 (spanning 2 versions)

Cytoscape 3.0 (and beyond) Development Modules

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.

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 with lots of feedback from others
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 definining and executing Tasks, configuring the Tasks, and supporting undo.
3.0 Status:	The API and implementation are largely complete.
Leading 3.0 work:	Pasteur, UCSD
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
Who did the work in 2.x:	UCSF, ISB
Module size:	Small
Module impact:	Medium

Bundles	Developers	Status
???	???	???

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:	UCSD, Pasteur, Toronto
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	???	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, Daniel Abel
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
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
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:	???
Who did the work in 2.x:	UCSD, 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:	???
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 (Alex Pico, Scooter Morris, Allan Kuchinsky)
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:	???
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
filters.old	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 (Alex Pico, Scooter Morris, Allan Kuchinsky)
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
Who did the work in 2.x:	UCSD
Module size:	Small
Module impact:	Small

Bundles	Developers	Status
merge	???	Incomplete, GSOC project

linkout

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

Bundles	Developers	Status
merge	???	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:	UCSD
Who did the work in 2.x:	MSKCC, Toronto, UCSD
Module size:	Small
Module impact:	Medium

Bundles	Developers	Status
webservices	Kei Ono (UCSD)	just proof-of-concept code
biopax	???	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:	UCSD(Kei, proof-of-concept code only)
Who did the work in 2.x:	UCSF, UCSD
Module size:	Small?
Module impact:	Small

Bundles	Developers	Status
scripting	???	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
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

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:	???
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

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
Who did the work in 2.x:	ISB, UCSD
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

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:	Farzana Kazi, George Wright (Bader lab) are 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
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:	it depends

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
Who did the work in 2.x:	everyone
Module size:	Small
Module impact:	Large

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:	???
Who did the work in 2.x:	everyone
Module size:	Large
Module impact:	Large

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
Who did the work in 2.x:	everyone
Module size:	Small
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:	???
Who did the work in 2.x:	Pasteur, ???
Module size:	Small
Module impact:	it depends

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)
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)

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

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:	???
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:	???
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)

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+||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|psi-mi]]||Piet Molenaar (AMC Amsterdam)||Incomplete, just starting||
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+||''Leading 3.0 work:'' ||Farzana Kazi, George Wright (Bader lab) are 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||
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||''Module size:''||Large  ||

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

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Diff for "Outdated_Cytoscape_3.0/DevelopmentModules"