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||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|sbml]] ||Noel Ruddock (Unilever) ||Incomplete, just starting || ||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|psi-mi]] ||Piet Molenaar (AMC Amsterdam) ||Incomplete, just starting || |
||[[http://chianti.ucsd.edu/svn/core3/sbml-impl|sbml-impl]] ||Jason Montojo (Toronto) ||Mostly done (needs visual property support) || ||[[http://chianti.ucsd.edu/svn/core3/psi-mi-impl|psi-mi-impl]] ||Jason Montojo (Toronto) ||Done || |
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| == shim == | == shim/plugin api == |
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||''Module impact:'' ||Medium|| ||'''Bundles''' ||'''Developers''' ||'''Status''' || || ''shim-api'' (not yet checked in) ||Mike Smoot (UCSD) ||Some basic interfaces have been proposed.|| || ''shim-impl'' (not yet checked in) ||Mike Smoot (UCSD) || A simple implemenation has been provided.|| |
||''Module impact:'' ||Large|| ||'''Bundles''' ||'''Developers''' ||'''Status''' || ||[[http://chianti.ucsd.edu/svn/core3/plugin-api/trunk|plugin-api]] ||Mike Smoot (UCSD) ||Some basic interfaces have been proposed.|| ||[[http://chianti.ucsd.edu/svn/core3/plugin-impl/trunk|plugin-impl]] ||Mike Smoot (UCSD) || A simple implemenation has been provided.|| |
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| ||''Leading 3.0 work:'' ||??? || | ||''Leading 3.0 work:'' ||Christian Lopes (UofT) || |
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| ||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|attribute-browser]] ||??? ||Incomplete || | ||[[http://chianti.ucsd.edu/svn/cytoscape3/trunk|attribute-browser]] ||Christian Lopes (UofT) ||Incomplete || |
Cytoscape 3.0 (and beyond) Development Modules
Contents
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:
- The API represents our best effort and we foresee no significant changes barring any strongly negative feedback.
- Each API module will include a default implementation to facilitate testing.
- Each API module will be fully documented with Javadoc.
- Each module will have a full suite of unit tests.
- Each API module has been through a formal code review.
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 |
Mike Smoot (UCSD) |
Requires some change based on mini-retreat feedback. |
|
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 |
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? |
|
Jason Montojo (Toronto) |
Mostly done (needs visual property support) |
|
Jason Montojo (Toronto) |
Done |
|
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 |
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 |
Mike Smoot (UCSD) |
Most interfaces have been specified |
|
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 |
Mike Smoot (UCSD) |
Some rough interfaces have been proposed. |
|
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 |
Mike Smoot (UCSD) |
Some basic interfaces have been proposed. |
|
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 |
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 |
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 |
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 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 |
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 |
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 |
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 |
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 |
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 |