By Randall Osborne
Genomica Corp., a bioinformatics company, came out of the gate strong as it nailed down its first two software licensing deals: one with Glaxo Wellcome plc and one with Oxagen Ltd.
Thomas Marr, president and chief scientist of Boulder, Colo.-based Genomica, spent 10 years developing the software system, called Discovery Manager.
Glaxo became involved in the early, testing stages of the system. Although it did not contribute funding, London-based Glaxo's requirements aided development.
"We knew they would push the limits of the software as hard as anyone," Marr said. "The tools had been developed for the average researcher. Everything [Glaxo] does is in large scale."
Discovery Manager, which went commercial in April, had to be adapted for Glaxo's high-throughput needs.
"We were able to do that quickly," Marr said. "We made major additions to the software in a couple of months, and I think that was one of the things that impressed them."
Glaxo's profit-making pharmaceutical work spurred other changes for the better in the software, which had been used purely as a research tool, he added.
"In an industrial setting, you need to harden it, make it bulletproof," Marr said.
Oxagen, of Abingdon, U.K., was founded in 1997 as a spin-out from The Wellcome Trust Centre for Human Genetics, a non-profit organization. A genomics company, Oxagen is "distantly related" to Glaxo Wellcome, but the two deals with Genomica are distinct, Marr said. Terms of neither agreement were disclosed.
Genomica's system lets investigators focus on several areas at once, unlike other software programs, which focus on a single aspect of gene discovery — typically, sequence analysis.
Population genetics and epidemiology tools allow for pedigree management, examining how a disease is distributed in a family. Associated phenotypes and genotypes can be stored. Genetic and physical mapping tools let researchers visualize and analyze complex relationships in data sets, and algorithms in the sequence analysis area provide for comparisons between self-generated and stored database sequences.
"It's all the little details," Marr said.
The "object-oriented" technology can mix and match data pieces — genes, DNA sequences, patients — to explore their relationships without wrestling with file format problems, as often arise when information bits are taken from varied sources.
"That was by far the largest single challenge," Marr told BioWorld Today. "We've solved that problem by putting a lot of blood, sweat and tears into it. We call it semantic normalization, and it was probably about half our research."
Marr developed the system with a team of researchers at Cold Spring Harbor Laboratory, in New York. It consists of a database server and a second server to run the analytic tools on a UNIX, PC or Macintosh desktop computer, which also can integrate the results from broad Internet searches.
Genomica, established in 1996, raised $7.5 million in private financing last October. Investors included Harris & Harris Group Inc., of New York, which owns about 10 percent of the company. *