Introduce the Ed Center on Computational Science

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Introduce the Ed Center on Computational Science
Engineering
Kris Stewart, DirectorEC/CSEstewart_at_sdsu.eduwww
.edcenter.sdsu.edu

• CSU Biology ChairsOctober 29, 1999

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What is Computational Science?
Science Discipline Physics, Chemistry, Biology,
etc.
Applied Mathematics Numerical Analysis, Modeling,
Simulation
Computer Science Hardware/Software
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What is Computational Science?
Teamwork and Collaboration
Science Discipline Physics, Chemistry, Biology,
etc.
Computer Science Hardware/Software
Applied Mathematics Numerical Analysis, Modeling,
Simulation
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the Grid
http//science.nas.nasa.gov/Groups/Tools/IPG
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Education Center on Computational Science
Engineering
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Mission

• Incorporation of tools for scientific
  investigation into the undergraduate curriculum
  preparing learners for post-Baccalaureate
• activities where
• Collaborative, interdisciplinary teams,
• Sophisticated computer tools and
• Effective communication
• are used in research and problem solving.

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Bioinformatics in the Post-Genome Era
The New Central Dogma
Genomes
Gene Products
Structure Function
Pathways Physiology
Scientific Challenges - Deciphering the genome,
mapping genotype-phenotype relationships,
dissecting organismal function, engineering
organisms with altered functionality,
understanding complex traits and
polymorphism. BIOINFORMATICS PROVIDES THE TOOLS
TO EXTRACT AND COMBINE KNOWLEDGE FROM ISOLATED
DATA AND RESULTS IN BIOLOGY INTO MEANINGFUL
WORKING MODELS OF CELLS AND ORGANISMS, THEIR
BIRTH, LIFE AND DEATH.
Source Eric Jacobson, NCSA
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The NCSA Information Workbench - An Architecture
for Web-Based Computing
NCSA Computational Biology Group
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Educational Workbench

• Interface Information Structure
• Student/TeacherCollaboration

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Common Portal Architecture
Portal Services
Browser
xml
Grid Middleware Fabric
Service Broker
xml
App
ORB
PDA
xml
App View Controller App Server
xml
Instrument
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Biological Portals
Protein Data Bank
the single international repository for the
processing and distribution of 3-D macromolecular
structure data
Biology Workbench
web-based tool for biologists allows biologists
to search many popular protein and nucleic acid
sequence databases. Database searching is
integrated with access a wide variety of analysis
and modeling tools, all within a point and click
interface that eliminates file format
compatibility problems.
http//biosync.sdsc.edu/
a portal for investigators planning visits to
synchrotron facilities and as a central resource
for researchers in structural biology seeking
information about such facilities.
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Computer Time at SDSC
Research Projects - peer reviewedyoull want to
have a code running so that you can makea
convincing argument for why you need the
additional computing power - UNIX
basedEducation Projects - expeditedwhen part
of a class, you can easily obtain 50 hoursof
time
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What can we collaborate on?