Cytoscape

This project was originally developed as a place to do experiments for Cytoscape. We highly advise you use Cytoscape for all your graphing needs.

Technology

The public API of GINY defines only interfaces. This is intentional so that a new implementation can be used seamlessly. One of the main focuses of this project is to make a "headless" mode available for graphing projects, and be able to move effortlessly to a visual mode.

The back-end of the package is currently using libraries from the CERN Colt project. Colt provides a high-quality, fast, set of data structures that seem to be missing from the regular Java libraries.

The visual side of GINY is implemented making extensive use of Piccolo. Piccolo is made by the Univerisity of Maryland under the supervision of Ben Bederson and seems to programmed mainy by Jesses Grosjean. Piccolo provides a very efficient ZUI. Piccolo has enabled us to create some very cool and useful nodes, especially for visualization of multi-dimensional information.

A number of our layouts are derived from implementations from the JUNG project. These layouts are annotated as such in the source code, and the JUNG license must be retained if making further derivitave of this code. The JUNG library offers a number of interesting ideas, and we hope to colloborate with them further in the future.

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A Sample Graph

Here is a Sample Graph, for lots more, go to the screenshots page.

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People

GINY was been developed primarily at the Instiute for Systems Biology. The primary developer is Rowan Christmas. Other ISBers involved have been Paul Edlefsen, Iliana Avila-Campillo and Larissa Kamenkovich. John Aitchison and Benno Schwikowski funded the project.
Some excellent work has also been done by Mike Smoot at the University of Virginia. In the true-open source spirit, Mike made his way to the project through Sourceforge, and has contributed invaluble code, especially involving the Edges.