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, MSKCC/Agilent (via changes to canvas object)

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: ???