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==== 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. |
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||''Description:'' ||A future project for a web front end for Cytoscape.|| ||''3.0 Status:'' ||None for the Cytoscape Consortium, but various member organizations are developing independent projects.|| ||''Who has done the work in 3.0:'' ||ISB, Toronto|| ||''Who did the work in 2.x:'' ||(didn't exist prior to 3.0)|| |
||''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 || |
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Cytoscape 3.0 (and beyond) Development 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.
model
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 |
work
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 |
logging
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 |
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. |
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 |
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. |
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 |
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. |
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 |
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. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
everyone |
Module size: |
Medium |
Module impact: |
Medium |
attribute-presentation
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 |
editor
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 |
layout
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 |
search/filters
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 |
groups
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 |
merge
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 |
linkout
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 |
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. |
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 |
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. |
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 |
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). |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
everyone |
Module size: |
Large |
Module impact: |
Large |
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. |
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 |
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. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
ISB, UCSD |
Module size: |
Large |
Module impact: |
Medium |
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: |
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 |
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. |
Who has done the work in 3.0: |
UCSD |
Who did the work in 2.x: |
everyone |
Module size: |
Small |
Module impact: |
Large |
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. |
Who has done the work in 3.0: |
??? |
Who did the work in 2.x: |
everyone |
Module size: |
Large |
Module impact: |
Large |
dev-process
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 |
usability
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 |
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 |
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 |
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 |
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 |
database-backend
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 |
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. |
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 |