Molecular and Genetic Bioinformatics
Facility (MGBF)
Director: Elliot J. Lefkowitz, PhD
Department/Center
Associations: Microbiology; Computer and
Information Sciences/Center for AIDS Research (CFAR);
Established:
1991
The UAB Molecular and Genetic Bioinformatics Facility
provides a variety of analytical software tools, biological databases, and
training and assistance opportunities to support the computer analysis of
genetic information by UAB researchers.
Facility Description
Location and Networking. The MGBF comprises a total of over 1,350 square
feet of space. All offices are in the
The MGBF maintains two computer
server rooms that are also located in the
Information Facilities (computer, software, and database). The UAB MGBF maintains a Sun quad-processor E450
Solaris server with 4 Gb of RAM and over 600Gb of disk
storage, and a Sun quad-processor V880 Solaris Server with 8 Gb of RAM and over 200Gb of storage to support the various
programs, databases, and analytical tools available to all UAB investigators. The MGBF provides UAB with the Genetics
Computer Group’s (now Accelrys)
For computationally intensive problems, including large
database searches, several high performance computing (HPC) clusters are available
on campus to support the needs of facility users. The UAB Department of Computer and Information
Sciences’ HPC infrastructure includes a 128 node compute cluster which has been
benchmarked at 1.41 Teraflops and provides 4 terabytes of storage. The Department also recently acquired a 13
megapixel, nine tile visualization wall that measures approximately 10' wide by
8' high. The unified image is created by
9 DLP projectors connected via optical DVI cabling to 5 rendering nodes in a
visualization cluster. All the clusters
are part of the CIS Grid Node, which is part of the distributed campus-wide
computational infrastructure - UABgrid.
The UAB School of
Engineering computing infrastructure includes a 128 node HPC cluster which has
been benchmarked at 1.1 Teraflops. Each
node consists of two 3.6 GHz Intel Xeon processors with 2 GB of memory. The nodes are all connected by gigabit Ethernet
and have 3 terabytes of attached storage. The
Research Information
Services. Access to computer hardware:
The facility provides access to the computer hardware described above to
support all computational needs of facility users.
Access to computer software: Shared access to the Wisconsin
Package sequence analysis software from Accelrys (formerly the Genetics
Computer Group) is available to all facility users. This package provides most of the genetic
analysis software tools necessary for a modern molecular biology laboratory. In addition to this set of analysis programs, this
package has been supplemented with a variety of other software tools that
provide additional analytical needs. These
include PAUP for phylogenetic analysis, and versions of BLAST and HMMPFAM
(database searching tools) that have been optimized to run on a computer
cluster (see above). Most users
currently access the GCG software through SeqWeb, GCG's web-based interface for
access to the Wisconsin Package and sequence databases.
Access to sequence databases and
other information resources: Sequence databases available locally include among others, the
Training in the use of hardware,
software, and information resources: Lectures in the practical application of bioinformatics
tools are given in several graduate-level courses including the Cellular and
Molecular Biology program’s Laboratory Methods course and the Advanced Human
Genetics course offered by the Department of Genetics. These lectures cover a basic introduction to
bioinformatics as well as practical applications of bioinformatics tools and
databases.
Personal assistance in solving
sequence analysis problems: The facility also provides personal assistance in solving individual
sequence analysis problems. This
assistance ranges from simple homology searches and sequence retrieval, to
phylogenetic analysis and mining of genomic information.
The
opportunity for collaborative research projects: Finally, the
bioinformatics facility also offers the opportunity to provide assistance in
the form of collaborative research projects. These collaborative projects involve more
complex analyses that frequently require a significant devotion of time and a
substantial knowledge of computer software and information resources in order
for a meaningful analysis to be performed.
Fees
Currently there is no charge for obtaining an account and
accessing the GCG sequence analysis programs through UAB’s site license. There is also no charge for an initial meeting
to discuss educational, training, and/or collaborative opportunities. Charges for subsequent services will be quoted
on a case-by-case basis.
Grant Support:
UAB Health
Services Foundation General Endowment Fund, 2000 – 2004
Contact Information:
Core Director: Elliot
J. Lefkowitz, PhD
Email: ElliotL@uab.edu
Phone: 205-934-1946
Web site: www.genome.uab.edu
Approved
by: Elliot J. Lefkowitz, PhD, Director
Date: March 11, 2008
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