Differences between revisions 3 and 13 (spanning 10 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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	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	???	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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	???
Who did the work in 2.x:	UCSD
Module size:	Small
Module impact:	Small

Bundles	Developers	Status
merge	???	Incomplete

linkout

Description:	An API that allows objects in Cytoscape to be linked to web databases.
3.0 Status:	Incomplete.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	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).
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	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
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	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.
Who has done the work in 3.0:	???
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
Who has done the work in 3.0:	UCSD (Kei. Proof-of-concept code only)
Who did the work in 2.x:	UCSF, MSKCC, Agilent
Module size:	Large?
Module impact:	Medium

Bundles	Developers	Status
decorated-networks	???	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
Who has done the work in 3.0:	Lead: 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.
Who has done the work in 3.0:	???
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.
Who has done the work in 3.0:	???
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 3 as of 2009-04-20 01:24:23 →
  Size: 6618
  Editor: adsl-75-17-114-73
  Comment:
+  ← Revision 13 as of 2009-05-15 10:13:00 →
  Size: 17255
  Editor: GaryBader
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
+==== 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.
-Line 4:
+Line 7:
-''Description:'' The core network and data table models used by everyone else.



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



''Who has done the work:'' UCSD with lots of feedback from others
+||''Description:'' ||The core network and data table models used by everyone else.||

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

||''Who has done the work in 3.0:'' ||UCSD with lots of feedback from others||

||''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 11:
+Line 19:
-''Description:'' An API for definining and executing Tasks, configuring the Tasks, and supporting undo.



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



''Who has done the work:'' Pasteur, UCSD
+||''Description:'' ||An API for definining and executing Tasks, configuring the Tasks, and supporting undo.||

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

||''Who has done the work in 3.0:'' ||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'''||

||[[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)||???||
-Line 18:
+Line 34:
-''Description:'' Both developer and user logging framework.



''Status:'' Incomplete.



''Who has done the work:'' ???
+||''Description:'' ||Both developer and user logging framework.||

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

||''Who has done the work in 3.0:'' ||Pasteur||

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

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

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



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

||???||???||???||
-Line 25:
+Line 45:
-''Description:'' APIs for importing and exporting data including networks, tables, sessions, and images.



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



''Who has done the work:'' UCSD, Pasteur, Toronto
+||''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.||

||''Who has done the work in 3.0:'' ||UCSD, Pasteur, Toronto||

||''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]]||???||Incomplete||

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|psi-mi]]||???||Incomplete||
-Line 32:
+Line 59:
-''Description:'' An API that '''''defines''''' the visualization of a network (and later table), but doesn't actually do the rendering.



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



''Who has done the work:'' UCSD, Daniel Abel
+||''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.||

||''Who has done the work in 3.0:'' ||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'''||

||[[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 39:
+Line 71:
-''Description:'' An API that modifies a view-model based on attribute (data table) values.



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



''Who has done the work:'' UCSD
+||''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.||

||''Who has done the work in 3.0:'' ||UCSD||

||''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 46:
+Line 85:
-''Description:'' An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model.



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



''Who has done the work:'' UCSD
+||''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.||

||''Who has done the work in 3.0:'' ||UCSD||

||''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 53:
+Line 101:
-''Description:'' An implementation that renders a data table.



''Status:'' Incomplete.  



''Who has done the work:'' ???
+||''Description:'' ||An implementation that renders a data table.||

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

||''Who has done the work in 3.0:'' ||???||

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

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

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



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

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|attribute-browser]]||???||Incomplete||
-Line 60:
+Line 112:
-''Description:'' A user interface that allows users to add, delete, and change nodes and edges in a network.



''Status:''  Incomplete.



''Who has done the work:'' Agilent
+||''Description:'' ||A user interface that allows users to add, delete, and change nodes and edges in a network.||

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

||''Who has done the work in 3.0:'' ||??? ||

||''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 67:
+Line 123:
-''Description:'' An API and several implementations of layout algorithms that modify the view-model for a given network.



''Status:'' Incomplete.



''Who has done the work:'' UCSF, UCSD
+||''Description:'' ||An API and several implementations of layout algorithms that modify the view-model for a given network.||

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

||''Who has done the work in 3.0:'' ||???||

||''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||
-Line 74:
+Line 136:
-''Description:'' An API and user interface that allows a network to be searched and/or filtered.



''Status:'' Incomplete.



''Who has done the work:'' UCSD
+||''Description:'' ||An API and user interface that allows a network to be searched and/or filtered.||

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

||''Who has done the work in 3.0:'' ||???||

||''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/cytoscape3/trunk|filters.old]]||Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)||Incomplete||
-Line 81:
+Line 149:
-''Description:'' An API and user interface that allows groups of nodes to be defined and captured as subnetworks.



''Status:'' Incomplete.



''Who has done the work:'' UCSF
+||''Description:'' ||An API and user interface that allows groups of nodes to be defined and captured as subnetworks.||

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

||''Who has done the work in 3.0:'' ||???||

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

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

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



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

||groups||???||Incomplete||
-Line 88:
+Line 160:
-''Description:'' An API that provides for set operations on networks based on attributes of the networks.



''Status:'' Incomplete.



''Who has done the work:'' UCSD
+||''Description:'' ||An API that provides for set operations on networks based on attributes of the networks.||

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

||''Who has done the work in 3.0:'' ||???||

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

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

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



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

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]]||???||Incomplete||
-Line 95:
+Line 171:
-''Description:'' An API that allows objects in Cytoscape to be linked to web databases.



''Status:'' Incomplete.



''Who has done the work:'' MSKCC, Agilent (support via right-mouse menu handler)
+||''Description:'' ||An API that allows objects in Cytoscape to be linked to web databases.||

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

||''Who has done the work in 3.0:'' ||???||

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

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

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



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

||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|merge]]||???||Incomplete||
-Line 102:
+Line 182:
-''Description:'' An API that provides a common interface for accessing web based interaction databases.



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



''Who has done the work:'' UCSD
+||''Description:'' ||An API that provides a common interface for accessing web based interaction databases.||

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

||''Who has done the work in 3.0:'' ||UCSD||

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

||''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||
-Line 109:
+Line 194:
-''Description:'' An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API.



''Status:'' Incomplete.



''Who has done the work:'' UCSD
+||''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.||

||''Who has done the work in 3.0:'' ||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||
-Line 116:
+Line 206:
-''Description:'' A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape").



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



''Who has done the work:'' UCSD
+||''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).||

||''Who has done the work in 3.0:'' ||UCSD||

||''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 123:
+Line 219:
-''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.



''Status:'' Incomplete.



''Who has done the work:'' ???
+||''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.||

||''Who has done the work in 3.0:'' ||???||

||''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||
-Line 130:
+Line 231:
-''Description:'' A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles.



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



''Who has done the work:'' UCSD
+||''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.||

||''Who has done the work in 3.0:'' ||UCSD||

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

||''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||
-Line 137:
+Line 244:
-''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."



''Status:'' Incomplete.



''Who has done the work:'' ???
+||''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||

||''Who has done the work in 3.0:'' ||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  ||
-Line 144:
+Line 252:
-''Description:'' The management and oversight of the overall Cytoscape architecture and how different modules interact with one another.



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



''Who has done the work:'' UCSD
+||''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.||

||''Who has done the work in 3.0:'' ||UCSD||

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

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

||''Module impact:''||Large  ||
-Line 151:
+Line 260:
-''Description:'' The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention.



''Status:'' Incomplete.



''Who has done the 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.||

||''Who has done the work in 3.0:'' ||???||

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

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

||''Module impact:''||Large  ||
-Line 158:
+Line 268:
-''Description:'' The management and oversight of the development processes, build tools, release tools and processes for Cytoscape.



''Status:'' Ongoing.



''Who has done the work:'' UCSD, ???
+||''Description:'' ||The management and oversight of the development processes, build tools, release tools and processes for Cytoscape.||

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

||''Who has done the work in 3.0:'' ||ISB, Toronto, UCSD||

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

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

||''Module impact:''||Large  ||
-Line 165:
+Line 276:
-''Description:'' The evaluation and refinement of Cytoscape usability including usability testing and tracking.



''Status:'' Inactive.



''Who has done the work:'' ???
+||''Description:'' ||The evaluation and refinement of Cytoscape usability including usability testing and tracking.||

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

||''Who has done the work in 3.0:'' ||???||

||''Who did the work in 2.x:''  ||Pasteur, ???||

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

||''Module impact:''||it depends  ||
-Line 171:
+Line 284:
-''Description:'' A future project for providing enhanced visualizations of networks in cytoscape with other background and foreground graphics and text (e.g. cell location).



''Status:'' Future project.



''Who has done the work:'' UCSF, MSKCC/Agilent (via changes to canvas object)
+||''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||

||''Who has done the work in 3.0:'' ||UCSD (Kei.  Proof-of-concept code only)||

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

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

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



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

||decorated-networks||???||Incomplete||
-Line 178:
+Line 295:
-''Description:'' A future project for a web front end for Cytoscape.



''Status:'' None for the Cytoscape Consortium, but various member organizations are developing independent projects.



''Who has done the work:'' ISB, Toronto
+||''Description:'' ||A web-based version of Cytoscape.||

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

||''Who has done the work in 3.0:'' ||Lead: 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  ||
-Line 185:
+Line 303:
-''Description:'' A future project that will provide a relational (or other) database backend for Cytoscape.



''Status:'' Future project.



''Who has done the work:'' ???
+||''Description:'' ||A future project that will provide a relational (or other) database backend for Cytoscape.||

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

||''Who has done the work in 3.0:'' ||???||

||''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 192:
+Line 314:
-''Description:'' A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities.



''Status:'' Future project.



''Who has done the work:'' ???
+||''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.||

||''Who has done the work in 3.0:'' ||???||

||''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"