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).
Background
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.
Procedure
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
|
Overview on biological data integration
- Data
integration and genomic medicine,
Brent Louie, Peter Mork, Fernando Martin-Sanchez, Alon Halevy, Peter Tarczy-Hornoch,
Journal of Biomedical Informatics, 40:5-16, 2007. [offcampus] [GS] - Addressing
the problems with life-science databases for traditional uses and
systems biology,
Stephan Philippi, Jacob Köhler,
Nature Reviews Genetics, 7(6):482-8, 2006. [offcampus] [GS] - Integration
of biological sources: current systems and challenges ahead,
Thomas Hernandez, Subbarao Kambhampati,
SIGMOD Record, 33:51-60, 2004. [offcampus] [GS]
Intro to biology
- Bioinformatics
- An Introduction for Computer Scientists,
Jacques Cohen,
ACM Computing Surveys, 36(2):122-158, 2004. [offcampus] [GS] - Life
and Its Molecules: A Brief Introduction,
Lawrence Hunter,
AI Magazine, 25(1):9-22, 2004. [GS]
Why graphics
InfographicsGraphicacy
Contact
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Class email list