Cytoscape Wiki|
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| ||''3.0 Status:'' ||The API and implementation are largely complete. || | ||''3.0 Status:'' ||The API and implementation are largely complete. API documentation and tutorial for Tasks completed. || |
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| ||[[http://chianti.ucsd.edu/svn/core3/work-headless-impl/trunk|work-headless-impl]] ||Samad Lotia (Pasteur) ||just beginning || | |
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| ||''3.0 Status:'' ||Incomplete. || | ||''3.0 Status:'' || Largely complete. Tutorial completed. || |
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| ||[[http://chianti.ucsd.edu/svn/core3/log-swing/trunk|log-swing]] ||Samad Lotia (Pasteur) ||In progress || | ||[[http://chianti.ucsd.edu/svn/core3/log-swing/trunk|log-swing]] ||Samad Lotia (Pasteur) ||Completed. || |
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| ||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|biopax]] ||??? ||Incomplete || | ||[[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 || |
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||[[http://chianti.ucsd.edu/svn/core3/layout/trunk|layout]] ||Mike Smoot (UCSD) ||Largely complete || ||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|automatic-layout]] ||??? ||Incomplete || |
||[[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|| |
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| ||''3.0 Status:'' ||Incomplete (~30% complete). ESP code will serve as API and Filters/quickfind will provide the UI. ESP code was ported to 3.0 and tested. || | ||''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. || |
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| ||''3.0 Status:'' ||Incomplete. || | ||''3.0 Status:'' ||Partially completed. || |
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| ||work.headless (TBD) ||??? ||Incomplete || |
||[[http://chianti.ucsd.edu/svn/core3/work-headless-impl/trunk|work-headless-impl]] ||Mathieu Michaud (Pasteur) ||Largely completed. || ||[[http://chianti.ucsd.edu/svn/core3/cmdline-application/trunk|cmdline-application]] ||Mathieu Michaud (Pasteur) ||Largely completed. || ||[[http://chianti.ucsd.edu/svn/core3/cmdline-parser-impl/trunk|cmdline-parser-impl]] ||Mathieu Michaud (Pasteur) ||Largely completed. || |
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| ||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]] || | ||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]] || |
Cytoscape 3.0 (and beyond) Development Modules
Contents
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 |
Mike Smoot (UCSD) |
Largely complete |
|
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 |
Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD) |
Largely complete |
|
Samad Lotia (Pasteur), Mathieu Michaud (Pasteur), Mike Smoot (UCSD) |
Largely complete |
|
Mike Smoot (UCSD) |
Largely complete |
|
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 |
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 |
Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD) |
Largely complete |
|
Brian Turner (Toronto), Samad Lotia(Pasteur), Kei Ono (UCSD), Mike Smoot (UCSD), ??? |
halfway? |
|
Noel Ruddock (Unilever) |
Incomplete, just starting |
|
Piet Molenaar (AMC Amsterdam) |
Incomplete, just starting |
|
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 |
Daniel Abel, Mike Smoot (UCSD) |
Largely complete |
|
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 |
Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD) |
more than halfway |
|
Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD) |
more than halfway |
|
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 |
Daniel Abel, Kei Ono (UCSD), Mike Smoot (UCSD) |
halfway |
|
Kei Ono (UCSD), Mike Smoot (UCSD) |
halfway |
|
Mike Smoot (UCSD) |
Largely complete |
|
Mike Smoot (UCSD) |
Largely complete |
|
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 |
??? |
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 |
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 |
Mike Smoot (UCSD) |
Largely complete |
|
Daniel Abel and Mike Smoot |
Largely complete |
|
Daniel Abel and Mike Smoot |
Largely complete |
|
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 |
Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD) |
Incomplete |
|
Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD) |
Incomplete |
|
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 |
??? |
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 |
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 |
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 |
Mike Smoot (UCSD) |
more than halfway |
|
Mike Smoot (UCSD) |
only an initial interface |
|
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 |
Peng Wang (UCSD) |
more than halfway |
|
Peng Wang (UCSD) |
more than halfway |
|
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 |
Mathieu Michaud (Pasteur) |
Largely completed. |
|
Mathieu Michaud (Pasteur) |
Largely completed. |
|
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 |