Recent trends in biological data integration

cse590q: Database Seminar (Winter 2008)
Wednesdays 4:30-5:20 in CSE 605 (database lab)

This winter quarter, the database seminar will focus on data management issues in life sciences. Primary organizer is Wolfgang Gatterbauer (gatter@cs).


Biological research is becoming increasingly data intensive. The outcome of individual experiments are generally large and diverse data sets. In order to build upon existing work and infer new insights, researchers want to integrate these heterogeneous data sets in some efficient way. This task, however, creates some serious data management issues such as how to ideally represent biological data and how to link different existing representations together in a way that scales.


Each class, a pair of two students presents either one longer or two shorter and related papers. Everyone reads the papers. One day before class, the presenters prepare and send out a one-slide graphical summary of their paper (Examples). Before last class, each pair prepares a one-slide graphical big picture summary of their view on the discussed papers at the end of the term (Examples). Hand drawings instead of computer drawings are fine and even encouraged.

Preliminary agenda

Date Paper(s) Presenters
Jan 9 Introduction to topic and organization of seminar Wolfgang
Jan 16 BioNavigation, BioGuide: University of Pennsylvania, Université Paris-Sud 11 Casey, Michal
Jan 23 Michigan Molecular Interactions: University of Michigan, Ann Arbor (OPTIONAL
Jan 30 Aladin: Humboldt University Berlin Vibhor, YongChul
Feb 6 BIOZON: Cornell Lynn
Feb 13 Gaggle: Institue for Systems Biology

Marianne, Bob

Feb 20 Bioverse: University of Washington Michal
Feb 27 Biomediator (U2): University of Washington Wolfgang
Mar 5 One-page summary slides and discussion All
Mar 12 no class -

Overview on biological data integration


Intro to biology

Why graphics



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