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:

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

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 (???)

Interest:

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)

???

Description:

Both developer and user logging framework.

3.0 Status:

In progress.

Leading 3.0 work:

Pasteur (Samad Lotia)

Interest:

Who did the work in 2.x:

UCSF, ISB

Module size:

Small

Module impact:

Medium

Bundles

Developers

Status

???

???

???

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)

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

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

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

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

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

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)

Interest:

Daniel Abel

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

Description:

An implementation that renders a data table.

3.0 Status:

Incomplete.

Leading 3.0 work:

???

Interest:

Who did the work in 2.x:

UCSD, others

Module size:

Small

Module impact:

Small

Bundles

Developers

Status

attribute-browser

???

Incomplete

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:

???

Interest:

Who did the work in 2.x:

Agilent

Module size:

Medium

Module impact:

Small

Bundles

Developers

Status

editor

Allan Kuchinsky (Agilent)

Incomplete

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)

Interest:

Pasteur (Benno Schwikowski)

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

Description:

An API and user interface that allows a network to be searched and/or filtered.

3.0 Status:

Incomplete.

Leading 3.0 work:

???

Interest:

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

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)

Interest:

Who did the work in 2.x:

UCSF

Module size:

Medium?

Module impact:

Medium

Bundles

Developers

Status

groups

???

Incomplete

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:

Who did the work in 2.x:

UCSD

Module size:

Small

Module impact:

Small

Bundles

Developers

Status

merge

???

Incomplete, GSOC project

Description:

An API that allows objects in Cytoscape to be linked to web databases.

3.0 Status:

Incomplete.

Leading 3.0 work:

???

Interest:

Who did the work in 2.x:

MSKCC, Agilent

Module size:

Small

Module impact:

Small

Bundles

Developers

Status

merge

???

Incomplete

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

Interest:

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

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

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

Interest:

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

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

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

Interest:

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

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

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

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

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

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

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)

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

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:

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

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:

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