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

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

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.

8:30 – 9:30 AM

Participant presentations

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

Lunch

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

4:00 – 5:30 PM

Group work

9:15 – 10:30 AM

Project presentations

Noon

Evaluation forms & new course suggestions