Workshop Announcement
Travel Directions


May 14 – 16, 2003

Chautauqua Short Course A–57


Wednesday, May 14th

8:15 8:25 AM

Registration in Room 337, McPheeter–Dennis Hall

8:30 8:40 AM

Welcome by Dr. Webb and Dr. Finkelstein of CAU

8:40 – 9:15 AM

Program Introduction
John R. Jungck

9:15 – 9:45 AM
HIV in Evolution
Sam Donovan

10 AM – Noon

Bioinformatics Problem Solving Session #1
Exploring HIV change within and between patients: Drawing biologically meaningful inferences from molecular data – forensics cases.
Sam Donovan and Tony Weisstein

Noon – 1:15 PM
1:15 – 2:30 PM

Toward a Theoretical Basis for Bioinformatics: Genetic Codes as Codes
John R. Jungck

Bioinformatics has largely been developed upon an empirical basis of statistical patterns; I believe that coding and information theoretical perspectives along with evolution and biophysics may help us develop a more theoretically grounded bioinformatics. Mathematical properties of genetic codes will be demonstrated with respect to their efficiencies, rates of transmission, detectability and correctability and of errors, symmetries, and origins by employing coding theory (Baudot codes, Gray codes, Hamming codes, Huffman Codes (Fractals and Power Laws), comma free codes, etc.), algorithmic complexity, abstract algebra, graph theory, combinatorics, information theory, and phylogenetic systematics of sequences. Genetic codes become much more understandable and elegant to biologists when they are not considered as mere ciphers, but are instead understood from three perspectives: codes per se, physical chemical interactions, and evolutionary selective pressures. In addition, I will illustrate some of the alternative distance metrics based upon different mathematical representations of genetic codes which have utility in genomic data base searching (comparative sequence analyses) and considerations of different evolutionary mechanisms.

2:30 – 3:30 PM
Problem Solving Session #2
Chimpanzee Conservation Genetics
Sam Donovan
3:30 – 4:30 PM
Group work
4:30 PM
Social hour

Thursday, May 15th

8:30 – 9:30 AM

Participant presentations

9:30 – 11:00 AM

Problem Solving Session #3
Protein Explorer with Enolase. Tia Johnson and Sam Donovan

11:00 – Noon

Problem Solving Session #4
Phylogenetic Trees: An introduction to understanding and teaching phylogenetic concepts and methods
Tony Weisstein

Noon – 1:15


1:15 2:30 PM

Multiple Sequence Alignment & Accelrys' GCG Wisconsin Package
Steven Thompson, School of Computational Science and Information Technology (CSIT), Florida State University, Tallahassee, Florida

2:45 – 3:45 PM

Problem Solving Session #5
Tree of Life: Exploring evolutionary relationships between bacteria using online sequence data from GenBank.
Sam Donovan, Tony Weisstein, Steve Thompson, Tia Johnson

3:45 4:00 PM

4:00 5:30 PM

Group work

Friday, May 16th

8:30 – 9:15 AM
Finish up group projects

9:15 – 10:30 AM

Project presentations

10:30 – Noon
Overview of BioQUEST Curriculum Consortium – BEDROCK (Bioinformatics Education Dissemination: Reaching Out, Connecting and Knitting–together)
Sharing information about personal projects and courses; how to contribute and stay involved; distribute additional papers and CDs; feedback and wrap–up
John R. Jungck, Tia Johnson, Sam Donovan, Tony Weisstein


Evaluation forms & new course suggestions

For more information please contact Sam Donovan or Sue Risseeuw (608/363–2012).

Sponsored by a grant from the National Science Foundation (DUE/CCLI-ND),
the BioQUEST Curriculum Consortium and

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