Genome Databases Seminar
Winter Quarter Schedule 2002
CS 545
Organized by:
Peter
D. Karp and
Gio
Wiederhold
TIME: Fridays, 3:15 pm until 4:30pm.
Please arrive 5 min. early to sign in!
LOCATION:
Stanford Quad, Bldg 370, Room 370;
DIRECTIONS: ASCII
Map
MAILINGLIST: Please send an email to
Marianne Siroker (siroker@cs.stanford.edu)
if you want to subscribe/unsubscribe to the mailing list for seminar
announcements.
POLICY: The Database Seminar is open
to the public
FURTHER INFORMATION: Please
contact Peter Karp: pkarp @ ai.sri.com
The theme of this quarter's CS545 is the databases that are being constructed in academic and commercial life-sciences organizations to manage genome data. Reading/demonstrations/analysis devoted to databases used to encode molecular-biology information, including DNA sequence, protein sequence and structure, gene expression, and other functional-genomics data. Emphasis is on representation and integration of the many diverse data sources, and their presentation for biomedical and pharmaceutical researchers. Issues: data structures and ontologies, cross referencing, quality control and error detection, search processes, suitability of different DBMSs, data provenance, and privacy protection for patient-derived information. Introduction and discussion by the instructors and presentations by experts from commercial and research organizations..
January 11, 2002
"Overview of Genome Databases"
Peter
D. Karp
Bioinformatics
Research Group, SRI International
[abstract] [powerpoint]
January 18, 2002
"Quantities and Precision"
Gio Wiederhold
Stanford University
"The EcoCyc and MetaCyc Pathway/Genome Databases"
Peter D. Karp
SRI International
January 25, 2002
"Scaling Genomics Data Integration -
Moving Bioinformatics into the Present"
Terence Critchlow
Lawrence Livermore National Laboratory
[abstract]
February 1, 2002
"Database Design - Data Modeling"
Iqbal Panesar
Incyte Genomics
[abstract]
February 8, 2002
"Gene Expression Data Management: Key Challenges and a Case Study"
Victor Markowitz
GeneLogic, Inc.
[abstract]
February 15, 2002
"Developments at the Protein Data Bank"
Phil Bourne
San Diego Supercomputer Center
[abstract]
February 22, 2002
"PharmGKB: The Pharmacogenetics Knowledge Base"
Daniel
Rubin
Section on Medical Informatics, Stanford University
[abstract]
[Presentation (pdf 0.82MB)]
March 1, 2002
"Integrated Data Systems for Interpreting Genome-Focused Data in
Cancer"
Ajay Jain
University of California, San Francisco
[abstract]]
[Presentation (pdf 5.3MB)]
March 8, 2002
"Model Organism Databases (and their Curation),
with a focus on the Saccharomyces Genome Database"
Michael
Cherry
Genetics Department,
Stanford University
[abstract]
[Presentation: Original (pdf 21.8MB);
Reduced (html 3.63M)]
March 15, 2002
"The Elucidation of Regulatory Networks in Complex
Biological Systems:
The Convergence of Biology, Medicine
and Computing"
George Poste
Health Technology Networks
[abstract];
[Presentation (Powerpoint 13MB)].
Last modified: 8 April 2002