Francis Crick Tribute
Monday, Aug 16, 2004 5:30 PM in Memorial Auditorium

High Performance and Grid Computing SIG
Tuesday, August 17, 2004 at 8:00 PM–9:30 PM in Memorial Auditorium
Chaired by Bob Lashley

Bioinformatics Education SIG
Tuesday, August 17, 2004 at 8:00 PM–9:30 PM in Building 200
Chaired by Yuying Gosser

The Bioinformatics Standards Committee (BSC) Panel discussion
Wednesday, August 18, 2004 at 8:00 PM in Memorial Auditorium
Led by Dr. John Wooley and Dr. George Michaels
See program outine below

The Bioinformatics Standards Committee (BSC) inaugural meeting
Thursday, August 19, 2004 at 12:00 PM–2:00 PM in Dohrmann Grove
Chaired by Phil Bourne

Francis Crick Tribute

Professor Gunther Stent, distinguished scientist from UC Berkeley, will talk about his work with Francis Crick. We will then show a video from Sydney Brenner, Nobel Laureate (2002), which he made for this event in Singapore. He will talk about his very close friend, Francis Crick when they were in Cambridge, UK during the Double Helix discovery.

High Performance and Grid Computing SIG - Meeting Agenda (PDF)

The appetite for computing cycles in Bioinformatics efforts continues to grow explosively. The High Performance Computing Special Interest Group of the CSB2004 has assembled a panel of industry and academia experts across various disciplines that contribute to the overall computing environment for Life Science. The panel will be addressing questions such as:

What is the direction of grid computing, SMP processing, memory architectures, storage systems, networks, databases, and algorithms and how do they support the analyses of today and the studies of tomorrow?

How do these computing needs impact, influence, or demand architectural decisions that are being made?

Come listen to the dialog and participate in the debate and discussion about the future of High Performance Computing as related to the information processing infrastructure of bioinformatics research and biotech applications.

SIG Co-Chairs:
• VK Holtzendorf - Life Science Strategic Program Manager, High Performance Computing Division, Hewlett-Packard Company

• Robert Lashley - Director of Ranch Technologies, Scalable Systems Group, Sun Microsystems Inc.

Panel Moderator:
• Rob Schreiber - Hewlett Packard Laboratories, Hewlett-Packard Company
Rob is known for research in parallel matrix computation and in compiler optimization. He is a contributor to the Matlab scientific computing environment, and is a co-developer of the High Performance Fortran programming language.

Panel Members:
• Walt Brooks - Director, NASA Advanced Supercomputing Division
As chief of NAS, Walt Brooks oversees all high performance computing work at NAS. During his early career he led groups that simulated and designed space science missions such as the Infrared Astronomical Satellite, the Space InfraRed Telescope Facility, and the Stratospheric Observatory for Infrared Astronomy. In 1993 he was selected to lead the Space Station redesign management team. He served as both Assistant Director of Aerophysics for Ames, and Chief of the Information Systems Programs and Projects Division before becoming acting NAS Division Chief in summer 1995. He received a doctorate in physics from Stevens Institute of Technology, performing research for his thesis at Brookhaven National Laboratory. In his copious spare time, he also earned a master's degree from the Stanford Graduate School of Business. His group is currently trying to put NASA back in the High End Computing business with the deployment of a 10,000 processor supercomputing system.

• Andrew Grimshaw - Professor of Computer Science, Director of the Center for Grid Research, University of Virginia
Dr. Grimshaw received his Ph.D. from the University of Illinois at Urbana-Champaign and then joined the University of Virginia where he is a professor of Computer Science. He is the chief designer and architect of Mentat and Legion – an early grid system, founder and CTO of Avaki, and the author or co-author of over 50 publications and book chapters. His research focuses on the development of software that is easy to use, supports large degrees of parallelism in applications code, and manages the complexity of the underlying physical system for the user.

• Grant Heffelfinger - Deputy Director for Materials Science and Technology in the Materials and Process Science Center, Sandia National Laboratories
Grant's graduate research in molecular physics led to a Ph.D. from Cornell University. Since then, he has held various staff and management positions at Sandia National Labs. Grant is the principal investigator for the Sandia-led US DOE Genomes-to-Life project focused on developing and prototyping computational biology tools for Synechococcus, an ocean bacteria which plays a significant role in the Global Carbon Cycle.

• Eamonn O'Toole - Senior Technical Staff Member, High Performance Computing Division, Hewlett-Packard Company
Eamonn works in the High Performance Computing Expertise Center and is the technical lead in Life and Materials Sciences. His role is to understand the application uses and needs of HP's customers in Life and Materials Sciences, and to use this knowledge to ensure that current and future HP systems and software are effective for these customers. Eamonn has extensive experience in LMS, working with application developers and users from industry and academia. He has contributed enhancements to a number of applications, including Gaussian and FASTA. In addition Eamonn works directly with HP's most important customers in LMS, including The Wellcome Trust Sanger Institute, Vital-IT and others, including in the past Celera Genomics. Eamonn holds a Ph.D. in chemical physics from Cornell University.

• Simon See - Sun Microsystems Inc.
Simon See is currently the High Performance Computing Technology Director for Sun Asia and also an Adjunct Associate Professor at Nanyang Technological University. Professor See is also the director for the Sun Asia Pacific Science and Technology Center. His research interests are in the areas of High Performance Computing, computational science, Applied Mathematics and simulation methodology. Dr. See graduated from University of Salford, UK, with a Ph.D. in electrical engineering and numerical analysis. Prior to joining Sun, Dr. See worked for SGI, DSO National Lab of Singapore, IBM and International Simulation Ltd, UK.

• Hans van Rietschote - Director, VERITAS Advanced Technology Group
Hans is responsible for scouting out new technologies that can enhance VERITAS' product portfolio. Hans has a Msc in applied Mathematics from the University of Twente in the Netherlands and a Masters in Business Telecommunication. Prior to joining VERITAS Hans worked at Origin Technology as business development director, at Philips software research center as a research group leader, and at AT&T Network systems in roles in engineering, customer support, product management and even sales. His current interests are: ubiquitous computing including ubiquitous access to one's data and "everything the open source community has to offer".

Revised 1/20/05

Bioinformatics Education SIG

Bioinformatics is a unique interdisciplinary field - drawing upon knowledge in computer science, mathematics and information science to address problems in biology and chemistry. Typical introductory courses available to undergraduates (biology, chemistry, physics, mathematics and computer science) do not include bioinformatics concepts and applications. This Special Interest Group will address bioinformatics in relation to undergraduate education by focusing on four fundamental questions:

• Is it important to engage undergraduates in bioinformatics, as future contributors to the field?
• How can students from all disciplines be introduced to bioinformatics at an early stage in their study?
• Is it practical?
• How can undergraduate students engage in bioinformatics related research?

The Pathways Bioinformatics Center at the City College of New York has conducted a sophomore level summer bioinformatics workshop for two years, finding that students from a variety of disciplines appreciate the introduction to Bioinformatics application and tool development, and once exposed are eager to join in research projects. Many other universities and colleges have conducted similar Bioinformatics workshops at different levels in the past few years.

The CSB2004 Bioinformatics Education SIG panel discussion will focus on ways to integrate exciting and pertinent bioinformatics research into the education and training of future scientists. All participants are encouraged to share ideas and experiences and layout a framework for the future of Bioinformatics Education.

The CSB2004 Bioinformatics Education SIG is chaired by Dr. Yuying Gosser, Research Assistant Professor, Director of the Pathways Bioinformatics Center, Department of Chemistry at the City College, The City University of New York (CCNY). Dr. Gosser is a NMR structural Biologist who sees the importance of bioinformatics in structural biology and molecular biology, attempting to integrate bioinformatics with experimental research practice. Her current research in Microarray gene expression analysis is in collaboration with Electrical Engineering faculty in the CCNY and the Molecular Pathology Laboratory at Memorial Sloan Kettering Cancer Center (MSKCC). Dr. Gosser’s goals are to develop Bayesian analysis based approaches for prediction of critical genes and their regulation in cancer development, to explore the target biomolecular systems with both Bioinformatics and structural biology technology, and to introduce Bioinformatics to undergraduate students at the early stage of their college education. Dr. Gosser received her Ph.D. in Physical Organic Chemistry from Brown University.

The Bioinformatics Standards Committee (BSC) Panel discussion and inaugural meeting

The IEEE Standards Association together with the Computational Systems Bioinformatics (CSB) committee have invited distinguished scientists to participate in a panel that will identify bioinformatics areas that need more specialized efforts for developing and testing data standards. The panel discussion will focus on prepared topics and answer questions from delegates. This event is supported in part by a grant from the Office of Science (BER), U.S. Department of Energy and the Hewlett-Packard Company.

The results of the panel discussions will be considered as guidelines for the Bioinformatics Standards Committee (BSC) inaugural meeting on Thursday 8/19/2004 from 12:00 PM to 2:00 PM in Dohrman Grove, Stanford University. The BSC is chaired by Phil Bourne, Professor in the Department of Pharmacology at the University of California San Diego and Director of Integrative Biosciences at the San Diego Supercomputer Center. The members will nominate and vote for BSC officers and work sheets will be distributed to the volunteers.

The rational for the establishment of the BSC is to provide a neutral forum for the global bioinformatics community to come together and work towards common agreements on standards. The IEEE Standards Association rules of consensus, due process and openness will be followed and guarantee the open access to the standards process, and will provide an appeal mechanism for anyone directly affected by the standard under development.

The panel will be led by Dr. John Wooley, Associate Vice Chancellor for Research at the University of California San Diego, an adjunct Professor in Pharmacology, and in Chemistry and Biochemistry, and a Strategic Advisor and Senior Fellow of the San Diego Supercomputer Center and Dr. George Michaels, PNNL Director of Bioinformatics for the Biomolecular Systems initiatives.

PROGRAM OUTLINE
5 min ----- opening remarks by computer architect Vicky Markstein, with a few observations on the benefits of bringing an engineer's methodology into the rapidly growing field of bioinformatics.

10 min ----- In a brief fashion, John will introduce the panel to the audience. Please send John a short paragraph of how you wold like to be introduced. (jwooley@ucsd.edu) This will be done for the entire panel at one time to sustain the flow of the panel's discussion later.

50 min ----- Each panelist (10 minutes each) will suggest a field in bioinformatics that would benefit the most if standards could be adopted. Please try to address the amount of time that it will take to develop a given standard, and then identify barriers to success and how they might be addressed.

x min ( where x is TBD but believe 10 - 15) ----- We propose allowing up to two questions per panel member either after each talk or perhaps after the 5 talks we can allow an initial 10 - 15 minutes for for questions that serve to amplify and clarify what has been discussed. John will try to set the boundaries about this initial discussion. Panel members are encouraged to ask questions at this point as well.

10 min ----- John will then ask the panelists to reach a consensus on prioritizing the list; particularly at issue is what standard to focus on first. This period should also provide a chance for panelists to query each other toward the prioritizations. If necessary , we will ask the audience to vote.

15-25 min ----- further Q&A, discussions , and comments from the audience.

Vicky will thank the panelists and invite everyone to attend the first BSC meeting on Thursday in Dohrmann Grove at noon.

Current Bioinformatics Standards panelists:
John Wooley, Panel Chair, Associate Vice Chancellor for Research at UC San Diego
George Michaels, VP and Associate Laboratory Director, PNNL
Sylvia Spengler, Program Director Science and Engineering Informatics, NSF
Richard Mural, Celera
Manfred Zorn, Director Bioinformatics, NIH
John Westbrook, co-Director, University of Rutgers
Suzanna Lewis, Program Analyst, Molecular & Cell Biology, UC Berkeley
Peter Karp, Director, Bioinformatics Research Group Artificial Intelligence Center, SRI