|| Jason Moore directs the Bioinformatics Core of the Program in Human Genetics.
The core’s 11 computer programmers provide database design services and support, Web interfacing, and software design in various programming languages.
group tackles range of computing needs
by Mary Beth
With its 11 computer programmers, the Bioinformatics Core is one
of the largest bioinformatics groups on the Medical Center campus.
The operation spans from the cores home base on the fifth
floor of Light Hall to the Information Technology Services networking
center on Peabody campus, where the VAMPIRE supercomputer is housed.
The Bioinformatics Core was organized by Jonathan Haines as part
of the Program in Human Genetics, and is under the scientific direction
of Jason Moore. The efforts of the facility are focused primarily
on genetics-related projects, though not exclusively.
Weve taken on a range of projects, from molecular genetics
to population genetics to genomics to microarray work, Moore
says. And were getting into proteomics now, too.
As part of the services offered, the staff programmers provide
database design services and support, Web page design and support
services, Web interface to the database, and software design in
various programming languages. Scheduling of programming and design
services can be arranged with Janey Wang, the cores manager.
In addition, the core manages Vanderbilts subscription to
the Celera database, and supports a wide variety of bioinformatics
software packages, such as the Wisconsin GCG Package for nucleic
acid and protein sequencing analysis. Charles Alexander, who is
responsible for this area of the cores services, conducts
training workshops and is available for one-on-one training in the
use of Celera and the various software products.
According to Moore, its a simple matter for the bioinformatics
core to coordinate services with other core facilities, such as
the Microarray Shared Resource. While the microarray core is responsible
for processing the raw data generated there and formatting it for
the researcher, the bioinformatics core is able to generate the
databases that facilitate analysis of the data.
For example, Moore and Shawn Levy, director of the Microarray Shared
Resource, are both principal investigators on a Program Project
Grant that Jacek Hawiger directs, which has as its goal to identify
markers of inflammation in the blood.
The group is trying to identify genes that are turned on
and off during the inflammatory process, Moore says. Were
working together to create a seamless database and analysis system
for that project, which will require a lot of microarray work.
Moore and his programmers have devised a number of computational
methods for analyzing microarray data and genetic epidemiological
data that wouldnt be possible, he says, without the use of
a supercomputer, such as VAMPIRE. With its 110 linked CPUs, VAMPIRE,
which stands for Vanderbilt Multiple Processor Integrated Research
Engine, provides the boosted speed and power needed to perform sophisticated
computations in a reasonable time frame.
One example of VAMPIREs power can be seen in its application
to the proteomics work of Richard Caprioli, whose lab is investigating
whether mass spectrometry can be used to correlate tumor proteins
with tumor grade. Comparing mass spectra of different tissue samples
to identify common proteins can be problematic, however, since the
protein peaks sometimes shift in a non-linear fashion. Moore devised
an algorithm that corrects for such shifts.
In the graphic depiction of results from this algorithm, identical
proteins appear as dots within vertical bins, the color of each
dot reflecting the relative abundance of that protein. Variation
in mass among the proteins is evident in the wobble
seen in the stacked tower of dots.
The algorithm must simultaneously figure out the optimal size of
the bins and what proteins belong in each. Analyzing 500 tissue
samples using this algorithm, as in one of Capriolis brain
tumor studies, can be computationally intensive, to say the least.
Even with VAMPIRE, it takes a couple of days to run the program;
without VAMPIRE, Moore says, it would be impossible.
Those responsible for VAMPIRE, including Alan Tackett, who has
direct oversight of the system, are anxious to give it more teeth.
Moore envisions a resource large enough to service the entire University.
Moore, along with Tackett and Paul Sheldon, a professor in the department
of Physics, have been marinating the idea of creating a scientific
computing center. Attempts to find the funding needed for this leap
include an application to the NIHs High End Instrumentation
Program, an NSF proposal, and a proposal to the Universitys
Academic Venture Capital Fund.
I think VAMPIRE will be a tremendous asset for anybody doing
computational studies, Moore says, not just in bioinformatics,
but across the university. The system will open doors for a lot
of people to do things they never dreamed they could do.