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Software aims to do for biotech scientists what word processing accomplished for writers
By ELLEN GOLDBAUM
Contributing Editor
While molecular biologists exploit state-of-the-art scientific equipment to discover the secrets of life and disease in the post-genomic era, they complain often that the software tools available to support these profound efforts are woefully inadequate.
A new software package under development by Virmatics, LLC., a spin-off company formed by researchers at UB and the Hauptman-Woodward Medical Research Institute, is about to change that radically, providing molecular biologists with the tools they need to design successful experiments, potentially boosting the pace of new drug discoveries.
"It's the difference between using a typewriter and a word processor," said Jeremy Bruenn, professor in the Department of Biological Sciences in the College of Arts and Sciences, comparing the software that he and Yangzhou Wang are developing to packages that now are available. Wang is a research scientist at the Hauptman-Woodward Medical Research Institute and research assistant professor of structural biology at UB.
Called The Virtual Cloning Suite, Virmatics' new software is designed to allow scientists to plan carefully their cloning experiments using a computer first, boosting the chances that their bench-top experiments will be a success.
A beta version of the software is expected to be ready this fall; a patent application has been filed.
"Think about this: What has word-processing done?" asked Bruenn. "It's made life much easier, people can create faster. In the same way, for molecular biologists who have good, creative ideas, The Virtual Cloning Suite will make their lives much more productive."
Every molecular biologist in the world is a potential customer for the software, said Bruenn, who has been discussing it with colleagues and peers at other institutions and in the private sector.
"When I tell them what our software can do, they salivate," he said.
While the need for improved molecular biology software is not new, Bruenn said that development of such products has taken on new urgency in the post-genomic era.
"Now that genomes have been sequenced, it's critical to find an automated way to plan cloning experiments," he noted. "Suppose you want to clone and express every protein gene in the human genome. Manually designing 60,000 primers would be truly unpleasant."
Currently, most biologists don't bother to use software to plan their cloning experiments, Bruenn said, because existing products are not very convenient.
"Many programs are very poor at doing what molecular biologists do on a daily basis," he said.
According to Bruenn, using one software package that is available commercially to create a virtual clone takes 45 steps and 45 minutes.
"Our program will take seven steps and do it in less than two minutes," he said. "And we'll have records of how we did it so we don't have to start all over next time we want to do the same thing."
The Virtual Cloning Suite will allow scientists to generate optimal virtual clones for the experiments they plan to perform.
A virtual clone, Bruenn explained, is a computer-generated assembly of DNA sequences that the scientist designs according to specific criteria based on the experiment that is being planned.
In the lab, the actual DNA sequence then is inserted into a vector, a self-replicating DNA molecule that can be introduced into appropriate cells for propagation, and is selected based on the type of experiment.
"A judicious choice of vector and method of insertion is required to achieve the desired result," Bruenn said.
He noted that most current software packages either don't have databases of vectors or the databases are incomplete and not annotated.
"How do you find the optimal system for your experiment?" asked Bruenn. "We are building into our software sufficient knowledge to give scientists some guidance, to give them the tools with which they can design decent experiments."
More robust and efficient experiments can have only a positive affect on numerous kinds of research that depend on increased knowledge of what genes do in cells, such as drug discovery through bioinformatics.
In addition to UB and HWI, Virmatics has received funding from the National Institutes of Health under the Small Business Innovation Research program, the UB Center for Advanced Technology, funded by the New York State Office of Science, Technology and Academic Research (NYSTAR) and the Western New York Business Development Fund.