Geodesic: A Distributed Annotation System (DAS) Client
Robin Dowell, Rodney M. Jokerst
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
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
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:firstname.lastname@example.org:/home/repository/biodas login
[give "cvs" as the CVS password]
cvs -d :pserver:email@example.com:/home/repository/biodas checkout geodesic
[creates the geodesic/ directory]
See the main DAS CVS website for information on
how to obtain the entire project.
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!
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
Current development goals:
See the TODO file for the most
up-to-date task list.
- Improve network failure management.
- Command line interface to hydra.
- Move from GET to POST in network requests
- Version parsing (for new versions of DAS specification)
- Improve usability -- eliminate jargon usage in interface
- Add Glyph Labeling
- Dynamic Zooming
- Dynamic Scrolling
- Graphical entry points display
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
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.
R. Dowell's Master's version (v0.3) February 2001
A Java 1.2 (Swing) version based on the DAS 0.94
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).
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, firstname.lastname@example.org
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