Open problems in bioinfo/compbio

Kevin Karplus karplus at
Sun Sep 26 12:47:16 EST 2004

In article <1095804620.536253.296740 at>, 
	yaoziyuan at wrote:
> I wonder what open problems there are in bioinformatics/computational
> biology? Which tasks are in need of an effective computer algorithm?

There are thousands of open problems in bioinformatics, but they have
mostly not been formalized.  Quite often the formalization of the
problem is the hard part, and the algorithms the easy part.
The problems change rapidly, as the biologists come up with different
data and ask different questions of it.

Bioinformatics is driven by the data, not the algorithms.  Get your
hands on some data and try to do something useful with it---you'll
probably need to apply some algorithms, possibly developing new ones,
in order to interpret the data.

There are, of course, some problems that have been around a long time
(like protein structure prediction, or finding the best multiple
alignment), but it is hard to make much progress on these, and showing
that you have requires more work usually than implementing the

Kevin Karplus 	karplus at
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Senior member, IEEE	Board of Directors, ISCB (starting Jan 2005)
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.

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