Biomedical Computation

Data and Collaboratories in the Biomedical Community Workshop

Funded by NCRR

View list of all presentations

LOCATION: ACCESS (Alliance Center for Collaboration, Education, Science, and Software)
Ballston Metro Center Office Tower
901 North Stuart Street, Suite 800
Arlington, VA 22203

Workshop Agenda

Monday, 16 September 2002

0800 – 0830 Continental Breakfast
0830 – 1015 Opening Session

View from NCRR: Michael Marron and other NCRR Staff (15 Minutes)
Introductions by Participants (30 Minutes)
Experiences with Collaboratories: Tom Finholt (30 Minutes)
Overview of Meeting: Peter Arzberger and Tom Finholt (15 Minutes)
Discussion (15 Minutes)

1015 – 1030 Break

1030 – 1130 Collaboratory Experiences, Part 1

The objective of these talks is to present vignettes of how the collaboratory enabled science that would not have happened otherwise, indicate where technology was not available that inhibited development, and suggest where collaboratories focused around data flow and resources would enhance science.

Experiences at PNL: James Myers (20 Minutes)
Experiences in a Clinical Setting: Steven Wolinsky (20 Minutes)
Q&A (20 Minutes)

1130 – 1245 Lunch

1245 – 1345 Collaboratory Experiences, Part 2: NCRR Collaboratories

The objective of this panel discussion is to review, on a case-by-case basis (no more than 10 minutes / 3 slides per project), the focus, the specific aims, and the results of NCRR supported collaboratories. After the presentations the discussion will address problems encountered, what collaboratories would do differently, and the evaluation criteria used by the projects.

  • Resource for Biocomputing, Visualization, and Informatics: Tom Ferrin
  • Interactive Graphics for Molecular Studies and Microscopy: Dianne Sonnenwald
  • High Performance Computing for Biomedical Research: David Deerfield
  • Macromolecular Modeling and Bioinformatics: Gila Budescu
  • National Center for Microscopy and Imaging Research: Mark Ellisman

1345 – 1615 Policy and Social Implications

Data sharing at NIH: what should be considered within the collaboratory: Wendy Baldwin (20 Minutes)
Evaluation: Gila Budescu (20 Minutes)
Social Informatics: Geoffrey Bowker (20 Minutes)
Q&A 30 min

1615 – 1630 Break

1630-1745 Key Data Projects:

The objective of this group of presentations is to discuss type of activities around data, and outline how collaboratory technologies could enhance these facilities and enhance the science conducts using these facilities.
Protein Data Bank: John Westbrook (20 Minutes)
SLAC: Peter Kuhn (20 Minutes)
Biomedical Informatics Research Network: Mark Ellisman (20 Minutes)
Q&A 15 min

1745 – 1800 Wrap-up, Overview of Day 2: Peter Arzberger and Thomas Finholt

1800 DINNER

Tuesday, 17 September 2002

0800 – 0830 Continental Breakfast

0830 – 1000 Technical Trends: Part 1

Over the next five years, what are the opportunities and limitations? What does the future hold, relative to collaborations around data resources and flows?
Cyberinfrastructure/Digital Library: Dan Atkins (20 Minutes – phone)
Grid: Computing and Data: Terry Disz (20 Minutes)
Grid: Path between grid and web services: Ian Foster (20 Minutes – vtc)
Data: Information Integration Technologies: Chaitan Baru (20 Minutes)
Q&A (10 Minutes)

1000 – 1015 BREAK

1015 – 1150 Technical Trends: Part 2

The Internet2 Commons H.323 Video Conferencing Service –
What it is and How to Use it: Bob Dixon (20 Minutes – vtc (need to move presentation to Monday afternoon)
Networking: Rick McMullen (20 Minutes)
Collaborative Tools: Jonathan Grudin (20 Minutes)
Semantic Web: James Hendler (20 Minutes)
Q&A: (15 Minutes)

1200 – 1300 LUNCH

1300 – 1330 Overview and Instructions for Breakout sessions

Envisioned are three parallel sessions, to address the following issues:

(1) What are the opportunities for using a collaboratory approach to deal with the problems associated with data in the biomedical community? What could such research catalyze?
(2) What could the biomedical community expect from another round of collaboratory investment by NCRR?(the time frame is 5 years)
(3) What should the goals of a collaboratory program be? How should a collaboratory program be evaluated? Potential evaluation metrics could include

(a) A measure of how small labs participate with larger labs in data sharing.
(b) A discussion of how to measure/ensure the availability of the products of a collaboratory program.
(c) Methods to ensure that a database of a certain size, with a projected growth rate is available to the community. What funding is available for such database maintenance programs?
Each group will be asked to present its findings the following day in power point or equivalent format.

1330 – 1630 Working groups

1630 – 1700 Preliminary Reports from Working Groups (problems, barriers, issues)

DINNER

Wednesday, 18 September 2002

0830 – 0900 Continental Breakfast
0900 – 1100 Full Feedback from Breakout Groups (30 minutes each) and discussion
1100 – 1115 BREAK
1115 – 1200 Overall summary of findings
1200 CLOSE of general meeting
1200 – 1700 Writing Group convenes

Thursday, 19 September 2002

Final Workshop Report

Presentation to the National Advisory Research Resources Council

PARTICIPANTS:

Peter Arzberger, National Biomedical Computation Resource, UCSD
Tom Finholt, School of Information, U Michigan
Dan Atkins, University of Michigan (phone)
Wendy Baldwin, Office of the Director, NIH
Chaitan Baru, San Diego Supercomputer Center, UCSD
Geoffrey Bowker, Department of Communications, UCSD
Gila Budescu, Resource for Macromolecular Modeling and Bioinformatics, University of Illinois
David Deerfield, High Performance Computing for Biomedical Research, PSC
Terry Disz, Argonne National Lab
Bob Dixon, Ohio State University (16, 18 September – vtc)
Mark Ellisman, National Center for Microscopy and Imaging Research, UCSD
Tom Ferrin, Resource for Biocomputing, Visualization, and Informatics, UCSF
Ian Foster, Argonne National Lab and U. Chicago (vtc)
Jonathan Grudin, Microsoft
Ted Hanss, Internet 2 (vtc)
James Hender, University of Maryland (17, 18 September)
Peter Kuhn, SLAC, Stanford
Donald F. (Rick) McMullen, Indiana University
Heather Miller, Office of the Director, NIH
James Myers, PNL
Steve Peltier, University of California San Diego (18 September)
Ralph Roskies, High Performance Computing for Biomedical Research, PSC (17, 18 September)
Dianne Sonnenwald, Interactive Graphics for Molecular Studies and Microscopy, UNC
John Westbrook, PDB, Rutgers
Steven Wolinsky, Feinberg School of Medicine, Northwestern University