Cytoscape Wiki
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. |
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 |
|
Samad Lotia (Pasteur) |
just beginning |
|
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), ISB |
Who did the work in 2.x: |
UCSF, ISB |
Module size: |
Small |
Module impact: |
Medium |
Bundles |
Developers |
Status |
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 |
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 currently porting to 3.0 |
Incomplete |
search/filters
Description: |
An API and user interface that allows a network to be searched and/or filtered. |
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. |
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: |
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), 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, 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: |
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 |