Genome Databases Seminar
Winter Quarter Schedule 2002
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 (firstname.lastname@example.org) 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
January 18, 2002
"Quantities and Precision"
"The EcoCyc and MetaCyc Pathway/Genome Databases"
Peter D. Karp
January 25, 2002
"Scaling Genomics Data Integration - Moving Bioinformatics into the Present"
Lawrence Livermore National Laboratory
February 1, 2002
"Database Design - Data Modeling"
February 8, 2002
"Gene Expression Data Management: Key Challenges and a Case Study"
February 15, 2002
"Developments at the Protein Data Bank"
San Diego Supercomputer Center
February 22, 2002
"PharmGKB: The Pharmacogenetics Knowledge Base"
Section on Medical Informatics, Stanford University
[Presentation (pdf 0.82MB)]
March 1, 2002
"Integrated Data Systems for Interpreting Genome-Focused Data in Cancer"
University of California, San Francisco
[Presentation (pdf 5.3MB)]
March 8, 2002
"Model Organism Databases (and their Curation),
with a focus on the Saccharomyces Genome Database"
Genetics Department, Stanford University
[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"
Health Technology Networks
[Presentation (Powerpoint 13MB)].
Last modified: 8 April 2002