May 9 2003 Biology workshop on Cray X1

Travel information

The meeting will be held onsite at ORNL.
If you have any comments or questions, please let me know.
    Regards,
    Mark Fahey faheymr@ornl.gov
    (865) 574-5622

Goals of Workshop

Computational Sciences:

1. Identify one or two important biology codes that are expected to benefit from vectorization
2. Identify people who will work on the optimization of these codes on the X1

Life Sciences:

1. Cray discuss what they have done with informatics algorithms to date
2. Demonstrate what non-traditional facilities can be accessed (i.e., all integer and word manipulation)

Cray:

1. Get a deeper understanding of ORNL's usage of applications in the life sciences. They would be interested in hearing from anyone using or developing applications for genomics, proteomics, or systems biology
2. Work with scientists who have bio applications believed to be well-suited for the upcoming X1 system, and to see how they might potentially assist in porting and optimizing those codes

Summary

Brief summary of the outcomes of this workshop is here.

Agenda

1060 Commerce Park Conference Room
8:00-9:00	Welcome and Cray X1 Overview and status	Mark Fahey
9:00-10:00	Biology and Informatics at Cray	Jim Maltby
10:00-10:30	Break
10:30-11:00	Genomes to Life	Al Geist
11:00-11:45	Cross-cutting needs GTL Facilities	and
	Transparent access to Supercomputers	Phil Locascio
11:45-12:15	PROSPECT and pathway codes	Ying Xu
12:15-1:15	WORKING LUNCH
Move to 6010 Conference Room
1:15-1:40	PICUPP and gene function codes	Nagiza Samatova
1:40-2:05	Protein complex using Rosetta	Andrey Gorin
2:05-2:20	MD simulation of biological molecules	Pratul Agarwal
2:20-3:00	discussion	Mark Fahey
3:00-4:30	Break
3:30-4:00	Biomedical analysis	Lee Hively
4:00-4:30	Biomechanics	Richard Ward
4:30-5:00	discussion and wrap up	Mark Fahey

Provided Equipment:

• Prox Projector

Invited Attendees

Jeff Nichols
Al Geist
Christy Adkinson
Jim Maltby
Andrey Gorin
Pratul Agarwal
Nagiza Samatova
George Ostrouchov
Phil Locascio
Ed Uberbacher
Ying Xu
Richard Ward
Trey White
Lee Hively
Kathy Fischer
Nancy Munro
Vladimir Protopopescu
Mike Leuze
Hooney Park
Gong-Xin Yu
Praveen Chandramohan
Rajesh Munavalli