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

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)

???

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

???

???

???

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

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

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

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:

Medium

Module impact:

Medium

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

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

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

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

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

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

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

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

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

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

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

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

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:

Incomplete.

Who has done the work in 3.0:

???

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

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

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

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

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

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

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

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

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