Genome Databases Seminar

Winter Quarter Schedule 2002
CS 545
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: Stanford Quad, Bldg 370, Room 370; DIRECTIONS: 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 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..

Seminar Schedule

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

February 1, 2002
"Database Design - Data Modeling"
 Iqbal Panesar
 Incyte Genomics

February 8, 2002
"Gene Expression Data Management: Key Challenges and a Case Study"
   Victor Markowitz
 GeneLogic, Inc.

February 15, 2002
"Developments at the Protein Data Bank"
Phil Bourne

 San Diego Supercomputer Center

February 22, 2002
"PharmGKB:  The Pharmacogenetics Knowledge Base"
   Daniel Rubin

 Section on Medical Informatics, Stanford University
[Presentation (pdf 0.82MB)]

March 1, 2002
"Integrated Data Systems for Interpreting Genome-Focused Data in Cancer"
   Ajay Jain

 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"
Michael Cherry

 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"
George Poste
 Health Technology Networks
[Presentation (Powerpoint 13MB)].

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.

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Last modified: 8 April 2002