Resources of the Molecular and Genetic Bioinformatics Facility (MGBF)

Director : Elliot J. Lefkowitz, PhD, Associate Professor of Microbiology

Department/Center Associations : Center for AIDS Research; Heflin Center for Human Genetics; Department of Microbiology; Department of Computer and Information Sciences

Established : 1991

Mission

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 sq. ft. of space. All offices are in the Bevill Biomedical Research Building (BBRB) which is located at 845 19th St. South in the middle of the UAB School of Medicine campus. All Offices are equipped with multiple gigabit and 100 megabit switched fast Ethernet connections to the building and campus network backbone. The campus network backbone consists of gigabit fiber connections linking each campus building to the campus computing center. UAB maintains OC-3 connections to the commodity Internet (I1). UAB is also a member of the Internet 2 (I2) consortium and maintains OC-12 connectivity to the Abilene network through Georgia Tech in Atlanta. I2 connectivity provides fast links to most major research universities in the country along with a number of government institutions including the National Center for Biotechnology Information (NCBI).

The MGBF maintains two computer server rooms that are also located in the Bevill Biomedical Research Building. Server room electrical feeds are entirely protected by the building’s emergency power generator in case of a failure in the electrical service to the building. The rooms contain multiple 20 and 30 amp 115 volt electrical feeds, as well as 30 amp, 220 volt outlets. Uninterruptible Power Supplies with battery backups are used between each of the electrical feeds and the server power supplies for every electrical connection. The main server rooms is provided with enhanced HVAC service and has a remotely monitored temperature sensor that sends an alarm to UAB’s Physical Security unit if the temperature exceeds a set threshold. Each server room contains its own Foundry Gigabit switch servicing all network connections. Each server is connected to an Avocent A2000R KVM over IP switch that allows for remote monitoring and control of all servers over a TCP/IP internet connection.

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) Wisconsin package of sequence analysis software tools. Our site-license for Accelrys includes access to the command-line, Xwindows-based ( SeqLab), and web browser-based (SeqWeb) interfaces to these sequence analysis programs. Dr. Lefkowitz also maintains over 20 other servers and workstations to support facility personnel including Dell PC servers, workstations, and laptops; Macintosh workstations; and Linux servers. All servers and workstations use either gigabit or 100 Mb cards for connection to the campus network. In addition, a Dell/EMC AX100 Storage Area Network with over 3 Terabytes of disk storage is used for file storage. Finally, the MGBF facility maintains a Dell PowerVault 132T tape library with two Quantum SDLT 320 drives for tape backups of all server, workstation, and database data.

For computationally intensive problems, including large database searches, several Linux-based computer clusters are available on campus that are available to support the needs of facility users. These include a 64 node, 128 processor cluster in the School of Engineering, and a 32 node, 64 processor cluster in the Department of Computer and Information Sciences. The School of Engineering Cluster will at least double in size over the next year, and the Computer Science cluster will increase to at least 120 nodes and 240 processors in the spring of 2005.

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 : Available sequence databases include all publicly available sequences in the GenBank nucleotide database, and the UniProt and GenPept protein databases.

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; the Advanced Human Genetics course offered by the Department of Genetics; Biochemistry’s Mass Spectrometry course; and the introductory Bioinformatics course offered by the Department of Computer and Information Sciences. 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 Center for AIDS Research, 1991 - 2008: NIH P30 AI027767

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

Website:www.genome.uab.edu

Approved by: Elliot J. Lefkowitz, PhD, Director
February 17, 2005