Cytoscape 3.0 (and beyond) Development Modules

Plan

3.0 development will proceed with a few distinct phases culminating in a complete set of modules that represent Cytoscape 3.0. In each phase we will deliver a specified set of modules that we declare to be "almost complete." This means:

Round 1 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. 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.

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

model-api

Mike Smoot (UCSD)

Requires some change based on mini-retreat feedback.

model-impl

Mike Smoot (UCSD)

Requires some change based on mini-retreat feedback.

events

Description:

The core event handling infrastructure 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

model-api

Mike Smoot (UCSD)

Largely complete

model-impl

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

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-tunable-props-impl

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

log-swing

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

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-impl

Jason Montojo (Toronto)

Mostly done (needs visual property support)

psi-mi-impl

Jason Montojo (Toronto)

Done

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

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

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.

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

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.

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

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

core tasks

Description:

Extensions of the Task interface defined in the Work module that represent different classes of tasks (Network task, NetworkView task, NodeView task, etc.).

3.0 Status:

An initial selection of core tasks has been specified along with many implementations.

Leading 3.0 work:

UCSD (Mike Smoot)

Interest:

Who did the work in 2.x:

everyone

Module size:

Large

Module impact:

Small

Bundles

Developers

Status

core-task-api

Mike Smoot (UCSD)

Most interfaces have been specified

core-task-impl

Mike Smoot (UCSD)

halfway

session

Description:

Defines the basic interfaces that define a Cytoscape "Session" including data structures like the list of networks and views.

3.0 Status:

A few interfaces have been defined based on 2.x session interfaces and Cytoscape.java methods.

Leading 3.0 work:

UCSD (Mike Smoot)

Interest:

Who did the work in 2.x:

everyone

Module size:

Medium

Module impact:

Medium/Large

Bundles

Developers

Status

session-api

Mike Smoot (UCSD)

Some rough interfaces have been proposed.

session-impl

Mike Smoot (UCSD)

Some basic implementations of the interfaces have been provided.

shim/plugin api

Description:

Provides a Java-only plugin interface to all 3.0 API.

3.0 Status:

A rough prototype has been written.

Leading 3.0 work:

UCSD (Mike Smoot)

Interest:

Who did the work in 2.x:

Sarah (Plugin Manager)

Module size:

Small

Module impact:

Large

Bundles

Developers

Status

plugin-api

Mike Smoot (UCSD)

Some basic interfaces have been proposed.

plugin-impl

Mike Smoot (UCSD)

A simple implemenation has been provided.

Round 2 Modules

attribute-presentation

Description:

Attribute browser. An implementation that renders a data table.

3.0 Status:

Incomplete.

Leading 3.0 work:

Christian Lopes (UofT)

Interest:

UCSD (Kei Ono)

Who did the work in 2.x:

UCSD (Kei Ono, Johannes Ruscheinski), others

Module size:

Small

Module impact:

Small

Bundles

Developers

Status

attribute-browser

Christian Lopes (UofT)

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

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.

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

layout-api

Mike Smoot (UCSD)

Largely complete

layout-cytoscape-impl

Daniel Abel and Mike Smoot

Largely complete

layout-jgraph-impl

Daniel Abel and Mike Smoot

Largely complete

layout-prefuse-impl

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

quickfind

Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)

Incomplete

filters

Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)

Incomplete

ESP

Maital Ashkenazi, Srinivas Vundavalli (GSOC), Peng Wang (UCSD)

Incomplete

search-API

Srinivas Vundavalli (GSOC)

Incomplete

search-UI

Srinivas Vundavalli (GSOC)

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

merge

???

Incomplete, Jianjiong Gao (GSOC)

linkout impl

Description:

An implementation of Linkout 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

linkout

Allan Kuchinsky (Agilent)

Incomplete

Round 3 Modules

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

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

webservices

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

application

Mike Smoot (UCSD)

more than halfway

session-api

Mike Smoot (UCSD)

only an initial interface

splash

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

ui2

Peng Wang (UCSD)

more than halfway

ui2-sdk

Peng Wang (UCSD)

more than halfway

ui2-sdk-scheduler

Peng Wang (UCSD)

more than halfway

Cytoscape 3 Plugin website

Peng Wang (UCSD)

incomplete

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

LD50 test framework

Mike Smoot

Write a set of unit tests that return a number where the number represents the number of objects/events/tasks that can be accomplished in 1 second. For instance how large of a network can be created in 1 second? How large of a network can be rendered in 1 second? How many equations can be applied in 1 second?

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:

An initial draft has been written.

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 work (Version 3.1 or Later)

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

work-headless-impl

Mathieu Michaud (Pasteur)

Largely completed.

cmdline-application

Mathieu Michaud (Pasteur)

Largely completed.

cmdline-parser-impl

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

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

Outdated_Cytoscape_3.0/DevelopmentModules (last edited 2011-02-24 15:35:42 by PietMolenaar)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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