BEDROCK Project Home Page
National Science Foundation
Howard Hughes Medical Institute Emory College Center for Science Education

Workshop Announcement


March 10 - 13, 2005

Woodruff Library
Room 215

Thursday, March 10th
6:00 PM
Welcome Reception Dinner
6:30 –- 6:45 PM
Welcome and Introduction to Emory, Pat Marsteller
6:45 –- 7:00 PM
Brief introduction to workshop
John R. Jungck, PI, BEDROCK
7:00–- 7:30 PM

Introduction to HIV Problem Space
Stephen J. Everse, University of Vermont

7:30 –- 7:50 PM
Introduction to Biology Workbench
Stephen J. Everse
7:50 –- 9:00 PM
HIV Problem Space Lab Work
Friday, March 11th
8:00 AM
Continental Breakfast
9:00 –- 9:45 AM
Overview of BioQUEST Curriculum Consortium
Ethel Stanley, Director of BioQUEST
9:45 –- 10:15 AM
Introduction to the Amylase Problem Space
Ethel Stanley
10:15 –- 10:30 AM
10:30 –- 11:30 AM
Amylase Problem Space Lab Work
11:30 –- 12:30 PM
Molecular Phylogenetics
John Jungck
12:30 –- 1:30 PM
1:30–- 2:00 PM

Intro to Metabolism: Databases and Modeling Problem Space
Raquel Holmes, BEDROCK Visiting Scholar from Boston University

2:00 –- 3:00 PM

Metabolism, Databases, and Modeling Problem Space Lab Work

3:00 –- 3:15 PM
3:15 –- 3:45 PM
Intro to Trp Cage Problem Space and Structural Bioinformatics
John Jungck
3:45 –- 4:15 PM
Trp Cage Problem Space Lab Work, Stephen Everse
4:15 –- 6:00 PM
Group Work and Poster Preparation
Saturday, March 12th
8:00 AM
Continental Breakfast
9:00 –- 10:00 AM
Poster Presentations on one of the first four problem spaces:
HIV, Amylase, Metabolism, or Trp Cage
10:00 –- 10:15 AM


10:15 –- 10:45 AM

Introduction to Transferrin Problem Space
Stephen J. Everse

10:45 –- 11:30 AM

Transferrin Problem Space Lab Work
Stephen J. Everse

11:30 –- 12:00 PM

Introduction to BEDROCK Web Pages and Uploading Projects
Stephen Everse

12:00 –- 1:15 PM

Lunch, group work and discussions
Developing bioinformatics curricula (decide on final project)

1:15 –- 2:30 PM

"A normal mode analysis for macromolecules using a driven molecular dynamics approach"
Martina Kaledin, Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University

The driven molecular-dynamics (DMD) method, recently proposed by Bowman et al., (J. Chem. Phys. 119, 646 (2003)), has been implemented into the TINKER molecular modeling program package. The DMD method yields frequencies and normal modes without evaluation of the Hessian matrix. It employs an external, harmonic driving term that can be used to scan the spectrum and determine resonant absorptions. The molecular motions, induced by driving at resonant frequencies, correspond to the normal mode vibrations. In the current work we apply the method to a 20-residue protein Trp-cage, that has been reported by Neidigh et al. (Nature Struct. Biol. 9, 425 (2002)). The structural and dynamical properties of this molecule, such as B-factors, root-mean square fluctuations, vibrational entropy and cross-correlations coefficients are calculated using the DMD method. The results are in very good agreement with ones calculated using standard normal–mode analysis method. Thus, the DMD method provides a viable alternative to the standard Hessian-based method and has considerable potential for the study of large systems, where the Hessian–based method is not feasible.

   2:30 –- 2:45 PM Break

Choice between two alternative sessions:

2:45 – 3:30 PM

3:30 – 4:00 PM

Introduction to Mapping & Microarray Problem Space
John R. Jungck

Maps & Microarrays: Benzer
Stephen Everse and John R. Jungck


2:45 – 3:15 PM

3:15 – 4:00 PM

Intro to West Nile Virus Problem Space,
Pat Marsteller and Raquell Holmes

West Nile Virus Lab Work,
Pat Marsteller and Raquell Holmes

   4:00 – 6:00 PM Group work and PowerPoint preparation
Sunday, March 13th
8:00 –- 9:30 AM
Continental Breakfast, Group work and PowerPoint/web form preparation
9:30 –- 11:00 AM
Web-based PowerPoint presentations (sharing projects and courses)
11:00 –- 11:15 AM
11:15 –- Noon
How to stay involved, feedback, sharing table (we will duplicate materials for participants), cut and distribute CDs, web sites & databases, collaboratories, other resources.

For more information please contact Sue Risseeuw (608/363-2012).

Sponsored by a grant from the National Science Foundation (DUE/CCLI-ND)

and the

 BioQUEST Home Page