Genome Databases Seminar

Spring Quarter Schedule 2003
CS 545G / BMI 345

Organized by: Peter D. Karp and Gio Wiederhold

Seminar Information

TIME: Fridays, 3:15 pm until 4:30pm. Please arrive 5 min. early to sign in!
LOCATION: Braun Auditorium, in Mudd Chemistry
(between Gates and the #1 Parking structure; across Campus Drive from the new Clark Center to be.)
DIRECTIONS: Transport and Parking options or a simple ASCII Map
MAILINGLIST: Please send an email to Marianne Siroker ( 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 @

The theme of CS545G is the databases that are being constructed in academic and commercial life-sciences organizations to manage genome data. Presentation, demonstrations, and analysis devoted to database issues specific to their use 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.

Seminar Schedule

April 4, 2003
"Overview of Genome Databases"
   Peter D. Karp
 Bioinformatics Research Group, SRI International
[abstract]   [powerpoint]

Of possible interest Thursday 1:00 to 5:00 pm Stanford-IBM BioX Symposium

April 11, 2003
"The EcoCyc and MetaCyc Pathway/Genome Databases"
Peter D. Karp
SRI International
[abstract]   [powerpoint]
  "Quantities and Precision"
Gio Wiederhold
Stanford University
SPEAKERS BELOW ARE TENTATIVE - based on the 2002 schedule -- and dates of their presentation are even more so

April 18, 2003
"The Encyclopedia of Life Project"
Phil Bourne
San Diego Supercomputer Center

April 25, 2003
"Data Integration and Management for Molecular and Cell Biology"
Barbara Eckman
IBM Life Sciences

May 2, 2003
"Integrated Data Systems for Interpreting Genome-Focused Data in Cancer"
Ajay Jain
University of California, San Francisco
[abstract] [PDF]

May 9, 2003
"PharmGKB: The Pharmacogenomics Knowledge Base"
Micheal Hewett
Stanford University

May 16, 2003
"Sharing Biomedical Data with Impunity"
Susan Davidson
University of Pennsylvania

May 23, 2003
"Integration Challenges for Gene Expression and Related Data"
Anthony Kosky
GeneLogic, Inc.

May 30, 2003
"Model Organism Databases (and their Curation),
with a focus on the Saccharomyces Genome Database"
Michael Cherry
 Genetics Department, Stanford University

June 6, 2003

Attendance at all but one session entitles enrolled students to 1 unit of credit.
By signing the attendance sheet circulated in class participants signify that they participated fully in that lecture. Signing and not participating is a breach of the Stanford Honor code.

ARCHIVE: Seminar information from Seminar Archive

[Stanford University | Computer Science Dep. | DB Home ]

Last modified: 8 April 2002