Genome Databases Seminar

Spring Quarter Schedule 2003
CS 545G / BMI 345

Organized by: Peter D. Karp and Gio Wiederhold

Seminar Information


T3:15 pm until 4:30pm. > Fridays, IME:
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 (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 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]

April 11, 2003
"The EcoCyc and MetaCyc Pathway/Genome Databases"
Peter D. Karp
SRI International
  "Quantities and Precision" [html]
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
"Scaling Genomics Data Integration - Moving Bioinformatics into the Present"
Terence Critchlow
Lawrence Livermore National Laboratory
[abstract]

April 25, 2003
"Gene Expression Data Management: Key Challenges and a Case Study"
   Victor Markowitz
 GeneLogic, Inc.
[abstract]

May 2, 2003
"Developments at the Protein Data Bank"
Phil Bourne
 San Diego Supercomputer Center
 [abstract]

May 9, 2003
"PharmGKB:  The Pharmacogenetics Knowledge Base"
   Daniel Rubin
 Section on Medical Informatics, Stanford University
[abstract]
[Presentation (pdf 0.82MB)]

May 16, 2003
"Integrated Data Systems for Interpreting Genome-Focused Data in Cancer"
   Ajay Jain
 University of California, San Francisco
[abstract]]
[Presentation (pdf 5.3MB)]

May 23, 2003
"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)]

May 30, 2003

June 6, 2003
   "The Elucidation of Regulatory Networks in Complex Biological Systems:
      The Convergence of Biology, Medicine and Computing"
George Poste
 Health Technology Networks
[abstract]; [Incyte interview]
[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