Workshop Announcement
Travel Directions



Thursday, April 3rd

4:30 6:00 PM

Welcome reception and introductions (light dinner provided)

6:00 6:15 PM

Welcome from Jeff Bond and Stephen Everse

Brief introduction to workshop, John R. Jungck, PI, BEDROCK

6:15 7:15 PM

HIV in Evolution
Sam Donovan, Director, BEDROCK
Tony Weisstein, Bioinformatics Research Associate, BEDROCK

7:15 7:30 PM

7:30 9:00 PM

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

Friday, April 4th

9:00 9:45 AM

Overview of The BioQUEST Curriculum Consortium and The BEDROCK Project
John R. Jungck and Sam Donovan

9:45 10:15 AM

Collaboratories: Models and Metaphors for Online Collaboration
Tia Johnson, Coordinator of Faculty Collaborations, BEDROCK

10:15 10:30 AM


10:30 11:30 AM

Bioinformatics Problem Solving Session #2
Mapping Multiple Sequence Alignments onto Structures with Protein Explorer
Tia Johnson and Sam Donovan

11:30 1:15 PM

Lunch and group work

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 2:45 PM


2:45 3:15 PM

Bioinformatics Problem Solving Session #3
Lisa Lambert, Associate Professor of Biology, Chatham College

"A case study in working with protein families"

Transferrins (TF) are a large family of iron binding proteins. There roles, however, appear to be quite diverse. Serum TF is the main iron transporter found in the plasma, whereas the function of lactoferrin (found in milk & other secretions) remains a mystery. The biological role of ovotransferrin (found in egg whites) appears to be one of protection. Our goal today will be to look at the structural similarities and differences to explore their functionally different roles.


3:15 4:30 PM
Group work and poster preparation

4:30 5:30 PM

Social hour

5:30 PM

Supper on your own

Saturday, April 5th

8:00 AM
Facilities open

9:00 9:45 AM

Group progress reports using mini-posters

9:45 10:45 AM
Structural Biology: Can we predict structures?
Stephen Everse, Assistant Professor, Department of Biochemistry, University of Vermont College of Medicine

Download the Powerpoint: everse_040503.ppt
Download the movies: N-lobe of serum transferrin, Superposition of N & C-lobes of transferrin

10: 45 11:00 AM


11:00 12:30 PM

Bioinformatics Problem Solving Session #4
Stephen Everse and Tony Weisstein

12:30 1:15 PM

Lunch and group work and discussions

1:15 2:15 PM

Navigating NCBI resources
Jeff Bond, Research Assistant Professor, Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine

The NCBI web site,, hosts a wide variety of data (including data related to scientific publications, biological sequences, structures, taxonomy, genetic disorders, and gene expression) as well as analysis tools. The talk will include a tour of NCBI resources that illustrates their usefulness in undergraduate research projects.

2:15 2:30 PM


2:30 3:00 PM
Introduction to web projects. Instructions on posting materials to be shared during the group session on Sunday.

3:00 5:30 PM

Bioinformatics Problem Solving Session #5
Open work session on the project of your choice
. Additional modules from which to choose:

  • One Cell Three Genomes
  • Glycosidases
  • Chimpanzee Conservation Genetics

5:30 PM

For those who are interested, we can have supper as a group.

Sunday, April 6th

8:00 AM
Facilities open.
9:00 10:30 AM
Group Presentations

10:30 12 PM

Open Discussion

  • Sharing information about personal projects and courses
  • How to contribute and stay involved
  • Distribute additional papers and CDs
  • Feedback and wrap-up

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,
The Vermont Genetics Network (VGN) - Biomedical Research Infrastructure Network (BRIN) and