[web-team] feedback from SVLUG website

Jim Kostecka jkostecka at ucsc-extension.edu
Fri May 16 11:37:30 PDT 2003


Bruce Moxon, whom I believe uses your website resources frequently, is
going to be teaching a class on Parallel and Distributed Computing for
Bioinformatics (using Linux).  He recommended that I contact your
organization to help get the word out about the class, which is
scheduled to start July 1st at UCSC Extension.  Please let me know the
best way to reach those members of your group who may be interested.
For your review I have included the course information below.

Thank you for your time and attention.  Any assistance you can provide
will be greatly appreciated.

Jim Kostecka
Program Representative
Bioinformatics Program
UC Santa Cruz Extension
(408) 861-3863
U N I V E R S I T Y O F C A L I F O R N I A E X T E N S I O N , S A N T

Parallel- and distributed-computing approaches have been instrumental in
accelerating the rate of discovery in the fields of genomics and
proteomics. Hundreds of thousands of hours of CPU time were used to
assemble the human genome alone. This massive scale of computation would
have been impossible just a few years ago. But recent advances in
parallel and distributed computing and the availability of inexpensive
supercomputer hardware
have not only made these approaches possible, but have placed them at
the heart of discovery in the post-genomic era.

Meanwhile, new computational challenges have arisen that will dwarf the
effort used to assemble the genome. High-profile biopharmaceutical
companies employ massively parallel-instrumentation technologies,
including microarrays, mass spectrometry, x-ray crystallography, and
bead-labeling and detection systems that generate very large datasets
(terabytes per day). More sophisticated computational models are
continually being developed to explore and explain the interactions of
proteins and their roles in cell metabolism. Contributing to the
advancement of this science is the widespread availability of
high-performance computing components. Cluster-computing solutions
employing high-performance networks and scalable storage components can
be built today through the “click-and-order” of components from computer
vendors’ Web sites. However, effectively harnessing the resources of
these Beowulf systems can remain a challenge for many organizations.

This course explores the basic principles of parallel- and
distributedcomputing systems, including shared- and distributed-memory
architectures and programming approaches. Case studies illustrating how
these systems are used effectively in bioinformatics applications are
presented. In addition, a range of approaches developed recently,
including distributed-component, Web services and shared-storage models
are covered. Through structured laboratory activities and student
projects, the theories presented are applied to real-world problems on
current parallel- and distributed-computing hardware and software

Prerequisite: Experience with UNIX/Linux or Windows development
environments (including shell scripting and Perl); completion of
“Bioinformatics Tools, Databases, and Methods,” “Introduction to
Programming for Bioinformatics II” or similar work experience. Consent
of the instructor is mandatory for students who have not completed the
two prerequisite courses.

REQUIRED TEXT: Beowulf Cluster Computing with Linux, Sterling, Thomas,
MIT Press.
X466.1 Computer Science (2)

The Instructor
BRUCE MOXON is a technology consultant specializing in the adoption and
deployment of strategic information technologies in largescale
information management and analysis solutions (an area he has termed
“high throughput
computing”). He has successfully applied this approach to largescale
gene-expression analysis, protein-function annotation and development of
Perlegen Science’s 100+ TB human-genome-variation (SNP) repository. Mr.
Moxon has worked with numerous high-profile commercial and
biopharmaceutical clients, including IBM, Bank of America, NASA,
Affymetrix, Celera Genomics, and Rosetta Inpharmatics, and is recognized
as a technology thought leader by prominent industry executives.

General Information
Fee: $645 ($710 if registering after June 17).
Location: UCSC Extension, Lab 139, 10420 Bubb Rd., Cupertino.
Date: 9 meetings: Tuesdays, 6–8:30 pm, July 1–August 26.
EDP 031X96 (use this EDP code to enroll)

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