Bioinformatics consultant Charles Alexander

BioInformation overload
by Leigh MacMillan

With the explosion of genome sequencing efforts, databases are becoming massive and more numerous. They include everything from gene and protein sequences to structure-function information, disease correlations, and population variations. In fact, they include every piece of information being gathered by the biological sciences.

The challenge is to put all of this information to use. That's where bioinformatics comes in.

Bioinformatics is a discipline that uses information technology and mathematical techniques to study patterns and datasets in biology, with the goal of determining characteristics of specific biological systems. The field is also referred to as biocomputing, computational biology, or genomics.

Help wading through the various bioinformatics tools is just a phone call (2-0855) or email (bioinformatics@vanderbilt.edu) away. On the other end of the line will be Charles Alexander, a bioinformatics consultant who arrived last year as part of the Program in Human Genetics computing/bioinformatics core. The division of Genetic Medicine and the Office of Research also participated in creating the position and recruiting Alexander.

"My job is to make bioinformatics software tools available, to show researchers how to use them, and to consult on the best strategies to answer different kinds of questions-to maximize usage of the tools and databases," Alexander said.

Alexander has set up a one-stop shopping bioinformatics website that is loaded with information about and links to various biocomputing resources. Get rid of all your individual bookmarks to Blast, FASTA, Entrez, NCBI, GenScan, ExPaSy, EBI/EMBNet....and bookmark just one site instead: www.vanderbilt. edu/bioinformatics/.

The major focus of current support at Vanderbilt is the Genetic Computer Group's (GCG) Wisconsin package. The package, referred to as GCG or the "Wisconsin" package, has over 100 programs that perform DNA/RNA and protein analyses.

The package can be accessed by a user-friendly web interface (SeqWeb) and by more versatile and comprehensive interfaces: SeqLab (X-Windows interface) and GCG shell commands. To set up a free account to access GCG, go to the bioinformatics website.

Through the core, investigators can also take advantage of reduced prices (below the standard academic discount price) for specific bioinformatics software, such as Vector NTI and OMIGA 2.0.

In addition to installing and maintaining the various bioinformatics packages and consulting one-on-one, Alexander offers regular workshops on how to use the packages.

Alexander recognizes that his efforts are a first step in biocomputing at Vanderbilt.

"We're trying to give researchers a basic repertoire of tools and software that they can use–that's our first goal," Alexander said. "Next we hope that they will come to us with specific kinds of questions that these tools don't help them solve, and we will write custom programs and packages to solve those questions."

The Program in Human Genetics computing/bioinformatics core offers additional services for genetic studies, including access to genetic pedigree analysis programs, high-end computing resources, and research database development and support.

Alexander received a degree in Biotechnology at the Rochester Institute of Technology. A self-professed "danger in the wet lab," he switched to bioinformatics and has essentially taught himself the computing side of the field. He is eager to see bioinformatics blossom at Vanderbilt and hopes that a training program will develop here.