Cytoscape 3.0 (and beyond) Development Modules
model
Description: The core network and data table models used by everyone else.
Status: The API and an implementation are largely complete.
Who has done the work: UCSD with lots of feedback from others
work
Description: An API for definining and executing Tasks, configuring the Tasks, and supporting undo.
Status: The API and an implementation are largely complete.
Who has done the work: Pasteur, UCSD
logging
Description: Both developer and user logging framework.
Status: Incomplete.
Who has done the work: ???
io
Description: APIs for importing and exporting data including networks, tables, sessions, and images.
Status: The API is largely defined, but all implementations need to be refined.
Who has done the work: UCSD, Pasteur, Toronto
view-model
Description: An API that defines the visualization of a network (and later table), but doesn't actually do the rendering.
Status: The API and implementation are largely complete.
Who has done the work: UCSD, Daniel Abel
vizmap
Description: An API that modifies a view-model based on attribute (data table) values.
Status: The API is largely complete and the user interface implementation is nearing completion.
Who has done the work: UCSD
presentation
Description: An implementation that renders (to screen, to image file, to ??) a network whose visualization is defined by a view-model.
Status: The API has been sketched and an implementation is in place, but it needs a lot of refinement.
Who has done the work: UCSD
attribute-presentation
Description: An implementation that renders a data table.
Status: Incomplete.
Who has done the work: ???
editor
Description: A user interface that allows users to add, delete, and change nodes and edges in a network.
Status: Incomplete.
Who has done the work: Agilent
layout
Description: An API and several implementations of layout algorithms that modify the view-model for a given network.
Status: Incomplete.
Who has done the work: UCSF, UCSD
search/filters
Description: An API and user interface that allows a network to be searched and/or filtered.
Status: Incomplete.
Who has done the work: UCSD
groups
Description: An API and user interface that allows groups of nodes to be defined and captured as subnetworks.
Status: Incomplete.
Who has done the work: UCSF
merge
Description: An API that provides for set operations on networks based on attributes of the networks.
Status: Incomplete.
Who has done the work: UCSD
linkout
Description: An API that allows objects in Cytoscape to be linked to web databases.
Status: Incomplete.
Who has done the work: MSKCC, Agilent (support via right-mouse menu handler)
webservices
Description: An API that provides a common interface for accessing web based interaction databases.
Status: Some work has been done, but incomplete.
Who has done the work: UCSD
scripting
Description: An API that allows scripts written in other programming languages (Python, Groovy, Javascript, etc.) to access and use the Cytoscape API.
Status: Incomplete.
Who has done the work: UCSD
swing-application
Description: A Java Swing-based desktop application for visualizing and analyzing networks (what everyone knows today as "Cytoscape").
Status: About 75% complete (excluding core plugins).
Who has done the work: UCSD
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.
Status: Incomplete.
Who has done the work: ???
plugin-manager
Description: A user interface for downloading, installing, automatic-update, and otherwise managing cytoscape bundles.
Status: The user interface is largely finished, but still needs to be integrated with the swing application.
Who has done the work: UCSD
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."
Status: Incomplete.
Who has done the work: ???
architecture
Description: The management and oversight of the overall Cytoscape architecture and how different modules interact with one another.
Status: It exists, but is poorly documented.
Who has done the work: UCSD
documentation
Description: The management and oversight of documentation for Cytoscape including the website, user manuals, tutorials, developer documents, wikis, and API documention.
Status: Incomplete.
Who has done the work: ???
dev-process
Description: The management and oversight of the development processes, build tools, release tools and processes for Cytoscape.
Status: Ongoing.
Who has done the work: UCSD, ???
usability
Description: The evaluation and refinement of Cytoscape usability including usability testing and tracking.
Status: Inactive.
Who has done the work: ???
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).
Status: Future project.
Who has done the work: UCSF
web-application
Description: A future project for a web front end for Cytoscape.
Status: None for the Cytoscape Consortium, but various member organizations are developing independent projects.
Who has done the work: ISB, Toronto
database-backend
Description: A future project that will provide a relational (or other) database backend for Cytoscape.
Status: Future project.
Who has done the work: ???
extended-cydatatable
Description: A future project that extends the interface for CyDataTable to allow things like joins and other relational database capabilities.
Status: Future project.
Who has done the work: ???