Geodesic: A Distributed Annotation System (DAS) Client

Robin Dowell, Rodney M. Jokerst

Description

The DAS is a client-server system similar to the current world wide web. The fundamental difference being that a DAS client retrieves information from multiple servers and integrates the data in a logical fashion. See the full specification for complete details.

NOTICE:

Geodesic was a prototype client for early versions of the specification.
It is NOT v1.01 compliant. Currently there are no plans to make it v1.01 compliant.

See the DasClient by Matthew Pocock or OmniDAS/OmniGene for more up to date DAS clients.

Anonymous CVS access

Geodesic is currently under heavy development so the CVS code base is expected to change rapidly, typically several times a day. While we try to keep the current version "working", we do not guarantee it will even compile.

Accessing the repository (example):

cvs -d :pserver:cvs@cvs.biodas.org:/home/repository/biodas login
[give "cvs" as the CVS password]
cvs -d :pserver:cvs@cvs.biodas.org:/home/repository/biodas checkout geodesic
[creates the geodesic/ directory]

See the main DAS CVS website for information on how to obtain the entire project.

Snapshots

We will periodically try to make available snapshot downloads of the Geodesic source code. These versions are known to compile using Sun's Java 1.2.2 on a Mandrake 7.2 Linux system. These are made available as an alternative to CVS, but should still be considered developmental code!

geodesic-2001-08-20.tar.gz

Documentation

Programmer's Notes

The code is composed of two separate major components: processing and visualization. The processing component, known as "Hydra", handles all non-graphical components of a client (querying servers, parsing XML replies, data integrity checking, etc). The visualization component, Geodesic, is responsible for communicating with Hydra to produce a user interface.

Current development goals:

See the TODO file for the most up-to-date task list.

Java & Portability

Geodesic is a Java application requiring Java 1.2 or better. Development has been under IBM's Java 1.2.2 on a Mandrake 7.2 Linux system.

We have tested IBM, Sun, and Blackdown Java versions. We do NOT recommend the Kaffe version of Java. All other conditions (platforms, Java versions, etc) have not yet been adequately tested.

For more information on Java and/or to obtain a Java Toolkit or Runtime Environment, go to Sun's Java website.

History

R. Dowell's Master's version (v0.3) February 2001
A Java 1.2 (Swing) version based on the DAS 0.94 specification.
This is the first version of Geodesic which is self-contained (does not depend on Neomorphic).
It is also the last version which assumes server side assembly (pre v0.95 of the specification).
initial prototype (v0.2) August 2000
A Java 1.1 (no Swing) version based on the DAS 0.9 specification which depends on the
Neomorphic Genome Software Development Toolkit (NGSDK).

Acknowledgements

Geodesic began in partial fulfillment of R. Dowell's Computer Science Master's degree at Washington University in St. Louis. This work was in collaboration with Lincoln D. Stein and Sean R. Eddy.

Robin Dowell, robin@genetics.wustl.edu
Sean R. Eddy Lab
Howard Hughes Medical Institute
Dept. of Genetics
Washington University in St. Louis
Last modified: Mon Feb 5 14:29:02 CST 2001