Biology
University of Houston
One platform integrates biology education and research
Reproduced with permission from NeXT
Computer, Inc.
A Reference
Guide to NeXT in Higher Education, Fall 1992
ยช
1992 NeXT Computer, Inc
"I'm addicted to NeXT computers," says Dan Davison,
assistant professor of biochemical and biophysical sciences
at the University of Houston. "They're a powerful,
cost-effective, easy-to-maintain UNIX machines. Plus, NeXT
has the apps we need-LISP, Sybase, and
Mathematica. In fact, in some situations, the
software is more valuable to me than the hardware."
In his undergraduate- and graduate-level introductory
courses in computational molecular biology, Davison uses
NeXT computers with MidasPlus, the molecular modeling
software created by scientists and programmers at the
University of California, San Francisco.
"We start the course using Macs; when we begin doing more
serious work, we get students on the NeXT machines, where
we use MidasPlus and public domain sequence analysis
software," explains Davison.
For the NeXT portion of the course, Davison assigns each
student a different data structure from the Brookhaven
Protein DataBank. Using MidasPlus, students display and
manipulate the molecule, determine its molecular size (lens
x width x size), mutate a residue, and then print
before-and-after pictures. "With this exercise, I'm trying
to get the students to see the changes a mutation can cause
in a protein," explains Davison. "Students gain a better
understanding of the molecules when they can look at them
from different angles with a three-dimensional model."
Davison also uses NeXT machines in his research work. For
example, using the Zilla application for distributed
computation, one of Davison's graduate students, Ed Chen,
has implemented a parallel distributed version of the
standard genetic sequence library search algorithm. The
algorithm parcels out searches to seven NeXT machines in
Davison's department. "With Zilla, it takes two hours
instead of all night for me to complete a search," he says.
"We have about three-quarters of the ability of a
supercomputer. In fact, overnight we can get the
performance of about 1 Cray X/MP processor with Zilla and
the NeXT machines."
Another project uses Lawrence Livermore Laboratory's genome
project data dictionary and tables with Sybase on the NeXT
machine to maintain the Chromosome 8 physical-mapping
database, a collaboration between Biology Department
faculty Dan Wells and Michael Wagner. "Sybase on the NeXT
offers us high performance, ease of use, and reliability,"
says Davison.
He recently started using Interface Builder to create
NeXTSTEP interfaces for programs he created on other
platforms before obtaining a NeXT machine. "Interface
Builder makes programming much more productive," he says.
"I'm able to write fewer lines of code, and I have
interfaces with a consistent functionality that are much
friendlier to use."
For more information, please contact:
Dan Davison
Assistant Professor of Biochemical and Biophysical Sciences
University of Houston
4800 Calhoun
Houston, TX 77204-5934
(713) 743-8366
davison@uh.edu