Build A Bioinformatics Supercomputer Using Grid Technology



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    Click here to view Bill Day's presentation slides.

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    Bill Day (bio), Staff Engineer and Technology Evangelist , Sun Microsystems
    Dr. Ferhat Hatay (bio), Product Line Manager, High-performance and Technical Computing Products & Solutions, Sun Microsystems
    Vijay Pande (bio), Assistant Professor of Physical and Biophysical Chemistry, Stanford University
    Stuart Jackson (bio), IT Architect, Incyte Corporation


    Program Overview

    This session will quickly review what grid computing is and how grids can be used to provide a relatively inexpensive environment for compute intensive tasks before diving into the meat of the matter, a how-to on setting up your own grid. We will detail the steps necessary to get started using the open source Grid Engine and the freely available Sun ONE Grid Engine which builds upon it. This talk serves as a 60 minute technical primer on a range of grid computing issues as well as a Grid Engine how-to. The talk will be followed by a panel discussion on several example applications of Grid Engine technology in bioinformatics.


    Speaker Bios

    Bill Day, Staff Engineer and Technology Evangelist, Sun Microsystems

    Bill created the J2ME Archive and Grid Archive to help developers build and deploy wireless and grid-enabled applications, respectively. He writes frequently about software development and has contributed feature articles to many sites and publications including, JavaWorld, Dr. Dobb's Journal Software Careers, and AT&T Wireless Developer.

    Bill serves as an Association for Computing Machinery Distinguished Lecturer and speaks often on wireless technology, grid computing, and system security. He has presented keynotes, technical sessions, and courses at major industry conferences including JavaOne, Software Development, and SIGGRAPH. He teaches Java and Wireless development as an extension instructor for the University of California Berkeley. Bill is also a Sun Certified Programmer for Java 2 Platform and Sun Certified System Administrator for Solaris Operating Environment.

    Prior to joining Sun, Bill was a software engineer at Silicon Graphics. Bill held fellowships with the Honeywell Technology Center, Edinburgh Parallel Computing Centre, and Lawrence Livermore National Laboratory. Bill earned a BS in Aerospace Engineering from the University of Oklahoma and completed one year of graduate studies in Scientific Computation while a National Science Foundation Graduate Research Fellow at the University of Minnesota.

    More information is available from Bill's site:

    Dr. Ferhat Hatay, Product Line Manager,High-performance and Technical Computing Products & Solutions, Sun Microsystems

    Dr. Ferhat Hatay is currently responsible as the product line manager for high-performance and technical computing products and solutions at Sun Microsystems. Prior to joining Sun, Ferhat was market development and performance engineering group leader with HAL Computer Systems. He was also a project leader and senior research scientist with NASA Ames Research Center working on parallelization of large scale scientific analysis packages. Dr. Hatay was a member of the NASA Ames Research Center team in 1998 to receive the NASA Software of the Year Competition Honorable Mention with OVERSET software environment for Computational Fluid Dynamic Analysis.

    Dr. Ferhat Hatay has extensive experience with applications of numerical solution techniques on the state of the art computing machinery for the problems of engineering and scientific interest. Ferhat's experience with parallel and distributed computing started with his appointment as a research fellow with NOAA Atmospheric Oceanographic and Meteorological Laboratory in Key Biscayne, Florida where he implemented data-assimilation techniques to the existing general circulation models of oceans. Ferhat received his PhD degree from Aerospace and Computational Sciences from University of Colorado at Boulder with graduate work also performed at Yale University and University of Miami in large-scale computer modeling and simulation. He developed control and optimization procedures in the computational modeling of physical and engineering design processes. His work covers several heat transfer and fluid dynamics areas including direct and large eddy simulations of transition and turbulence in incompressible and compressible flows, design of low-gravity heat transfer test cells, magnetohydrodynamics, cooling of electronic components, cardiovascular and cardiorespiratory fluid dynamics modeling, and atmospheric flow simulations. His one proud accomplishment is to have designed and taught Numerical Computations course for graduate and undergraduate engineering students.

    Vijay Pande, Assistant Professor of Physical and Biophysical Chemistry, Stanford University

    Prof. Pande's current research centers on the development and application of novel grid computing simulation techniques to address problems in chemical biology. In particular, he has pioneered novel distributed computing methodology to break fundamental barriers in the simulation of kinetics and thermodynamics of proteins and nucleic acids. As director of the Folding@Home and Genome@Home projects, Prof. Pande has, for the first time, directly simulated protein folding dynamics with quantitative comparisons with experiment, often considered a "holy grail" of computational biology. His current research also includes novel simulation methods for high precision drug binding affinity calculations,protein design, and synthetic bio-mimetic polymers.

    Prof. Pande received a BA in Physics Princeton University in 1992. There, he was first introduced to biophysical questions, especially in his undergraduate thesis research with Prof. Philip Anderson, a Nobel Laureate in physics. Three years later, he received his PhD in physics from MIT, studying as a NSF Fellow under Profs. Toyoichi Tanaka and Alexander Grosberg. At MIT, Prof. Pande's research centered on statistical mechanical models of protein folding and design, suggesting novel ways to design protein sequences to have the desired stability and folding properties. As a Miller Fellow working with Prof. Daniel Rokhsar at UC Berkeley, Prof. Pande extended this methodology to examine atomistic protein models.

    Prof. Pande has won numerous awards, including most recently being named to MIT's TR100 (top young innovators in 2002), a Frederick E. Terman Fellowship (2002), and a Henry and Camile Dreyfus Teacher-Scholar (2003). Prof. Pande is currently an Assistant Professor of Chemistry and (by courtesy) of Structural Biology.

    Stuart Jackson, IT Architect, Incyte Corporation

    Stuart, currently an IT Architect for Incyte Corporation, brings his 20 years of bioanalytical and bioinformatics computing experience to the challenges in today’s fast paced technological environment. Born and raised in California’s Silicon Valley, he has witnessed and participated in the computing revolution that is shaping the 21st century.

    After receiving his B.S. in Biochemistry from the University of California, Stuart worked in the Biomedical Research Laboratory at SRI International. In the environment of the 1980’s, he found a wonderful opportunity to use his computing talent to automate data acquisition and analysis for projects in drug metabolism and enzymology.

    Stuart next joined Syntex, a pharmaceutical company, and there moved firmly into the IT arena as Manager of Laboratory Automation for Research Information Systems. Working in a GMP environment (Good Manufacturing Practices, a set of government regulations applicable to the manufacture and testing of drugs intended for human use), he became an expert in the validation and operation of regulated computer systems. Stuart boasts an unblemished record in over 20 FDA inspections in an era of increasing focus on the reliability of automated systems used in the pharmaceutical industry.

    Stuart joined Incyte Genomics in 1997, and was given the mission to alter the computing paradigm at Incyte from a minicomputer-based infrastructure to one based on low cost, commodity computing clusters. In the space of less than two years, his team created and productionalized a software system to distribute data processing over very large clusters of Linux-based microcomputers. This paradigm shift realized a huge reduction in the computing costs associated with the production of Incyte’s database products.

    Event Logistics


    Cubberley Community Center, Theater
    4000 Middlefield Road
    Palo Alto, CA


    6:30-7:00pm Registration/networking
    7:00-8:30pm Program


    Early Bird Registration (by June 13)

    $15 SDForum Members and Sun Microsystem Employees and MITCNC Members
    $30 Non Members

    Regular Registration (after June 13)

    $25 SDForum Members, Sun Microsystems Employees and MITCNC Members
    $40 Non Members

    Pre-registration for this event is closed.
    Please register at the door.