Although this event is now over, please feel free to browse the links below
to familiarize yourself with the many valuable resources coming out of this workshop.

Workshop Announcement
Travel Directions



Thursday, October 17th

4:30 6:00 PM

Welcome reception and introductions (light dinner provided)

6:00 6:15 PM

Welcome from Peder Jungck, Founder, CloudShield

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

6:15 7:15 PM

Dr. Aviv Bergman, Stanford University
Center for Computational Genetics and Biological Modeling

"Gould's punctuation verses Waddington's canalization:
A look at micro and macro evolutionary processes"

Despite abundant genetic variation and diverse environmental conditions phenotypic variation is generally low within a species. Waddington termed the buffering of developmental processes against genetic and environmental variation canalization. Gould emphasized rapid transitions in form and function as an important factor in the evolutionary record. This talk will use these two contexts to discuss micro and macro evolutionary mechanisms that extend basic notions of Darwinian selection.

Dr. Bergman is the co-director of the Center for Computational Genetics and Biological Modeling at Stanford University. The research agenda for the center involves interdisciplinary research into quantitative problems of biology that can be attacked using a combination of computational and mathematical tools. Article featuring Dr. Bergman in the Stanford Report.

7:15 7:30 PM

7:15 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, Director, BEDROCK

Friday, October 18th

9:00 9:45 AM

Overview of The BioQUEST Curriculum Consortium and The BEDROCK Project

9:45 10:15 AM
Introduction to web projects & databases
Amanda Everse, Administrator, BioQUEST web site

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, Director of Collaboratories, BEDROCK 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 3:45 PM

Bioinformatics Problem Solving Session #3
Studying One Cell with Three Genomes
Sam Donovan, John R. Jungck, Tia Johnson, and Stephen Everse

3:45 4:30 PM
Group work and poster preparation

4:30 5:30 PM

Social hour

5:30 PM

Supper on your own

Saturday, October 19th

8:00 AM
Facilities open

9:00 9:45 AM

Group progress reports using mini-posters

9:45 10:15 AM
Collaboratories: Models and Metaphors for Online Collaboration
Tia Johnson

10: 15 10:30 AM


10:30 11:30 PM

Bioinformatics Problem Solving Session #4
John R. Jungck and Tia Johnson

11:30 1:15 PM

Lunch and group work and discussions

1:15 2:45 PM

Dr. Stephen J. Everse, Department of Biochemistry
College of Medicine, University of Vermont

"Transferrin: Not your average protein"

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.

Dr. Everse received his Ph.D. in Chemistry from the University of California, San Diego in 1995. His postdoctoral work at UCSD focused on obtaining a structural understanding of the fibrinogen molecule. His work resulted in the X-ray crystallographic structures of the fibrinogen fragment D and the fibrin fragment double-D. He joined the Biochemistry department in the Fall of 1998 as part of the HHMI structural biology initiative at UVM.

2:45 3:00 PM


3:00 4:30 PM

Bioinformatics Problem Solving Session #5
Transferrins: A case study in working with protein families

5:30 PM

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

Sunday, October 20th

8:00 AM
Facilities open
                                  Short reports on group projects and next steps
9:00 9:20 AM
Group A
9:20 9:40 AM
Group B
9:40 10:00 AM
Group C
10:00 10:20 AM
Group D

10:20 10:30 AM


10:30 12 PM

  • 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, and assisted by CloudShield Technologies, Inc.