Skip to main content
Premium Trial:

Request an Annual Quote

Seattle Bioinformatics Startup Geospiza Aims for Survival Among the Sequencers

Premium

SEATTLE--"The essence of bioinformatics is that sequences evolve," said Todd Smith, president of bioinformatics consulting and contracting startup Geospiza, explaining his choice for his company's name. "Geospiza is the genus name for the ground finches that inhabit the Galapagos islands," he said. While Smith picked the name for its allusion to Darwin's groundbreaking research on evolution in the South Seas more than a century ago, his company is focused on cutting-edge technology that aims to contribute to the future of genomic research.

During an interview with BioInform last month, 37-year-old Smith, dressed Seattle-casual in a blue tie-dyed T-shirt, said, "Our goal is to enable biologists to use state-of-the-art software to make discoveries in DNA sequences. When delivered in a useful way, biologists love it because they get their work done faster."

Smith, who holds a PhD in medicinal chemistry and has 15 years' experience with biochemical and recombinant DNA sequences, is primarily responsible for Geospiza's business development and sales. His partners include software engineer Joe Slagel, 29, who formerly developed tools to graphically display genome information and analysis results at the Institute for Genomic Research and the University of Washington, and codewriter Dave Campbell, 36, who joined the company last month with a background in biochemistry and computer sciences.

The Finch-Suite, a client-server software system, is the foundation of Geospiza's platform. Its components manage and analyze data associated with high-throughput DNA sequencing, storing analysis results in an embedded relational database management system to provide high-level and drill-down summary reports that are accessed through a web browser. A structured query language interface gives clients the ability to develop custom reports.

The Finch-Chromatogram Server stores, manages, and archives chromatogram files from automated DNA sequencers. It features a web-based interface, a phred basecalling algorithm, and the ability to operate on low-cost computers running Linux.

"Anyone sequencing DNA will spend between $10 and $15 per sequence collecting raw data," Smith postulated. "An equal investment is required to analyze these data. With today's technology, a laboratory can easily determine over 100 sequences a day." The Finch-Chromatogram Server, he said, is designed to protect that investment.

The Finch-BLAST Server is a preconfigured system "well-suited for customers who want an in-house solution," Smith contended. Data are submitted and viewed through web browser applications. The server saves time and money, Smith asserted, through rapid deployment and by running on inexpensive hardware with low maintenance costs.

Smith said he plans to center Geospiza's activities around the Finch-Suite system. "In the short term we want to turn the chromatogram server into a robust product, to sell it to laboratories involved in production sequencing, pharmaceutical and biotechnology companies, and academic laboratories involved in genome projects," he explained.

Having no local bioinformatics competition, the self-financed Geospiza, which has received cooperative academic grants from the National Institutes of Health and the National Science Foundation, has been a contender for contracts with some of the area's prolific sources of genetic information. Since Geospiza hung out its shingle in November 1997, customers have come to include immunologist and human genome project researcher Leroy Hood at the University of Washington's Genome Sequencing Center, the Fred Hutchinson Cancer Research Center, and contract research firm MDS Panlabs in Bothel.

National competition is stiffer, Smith said. Finch-Suite features components that rival Perkin-Elmer's BioLims package and Pangea Systems' GeneMill, he claimed, adding, "One of the things that distinguishes us from the competition is that we're not looking toward comprehensive analysis solutions. Rather, we're looking for specific solutions that solve particular problems."

Geospiza's clients applaud the vendor's hands-on customer service approach. Project manager John Verburg of biotechnology services at MDS Panlabs said he began working with Geospiza in its infancy. "Todd and Joe have made sure that our system is customized in a way that meets our needs, unlike other companies that might offer a fixed menu of choices where you sort of have to make do," Verburg said.

"I like their approach and they are responsive," agreed Lee Rowen, director of the multimegabase sequencing center at the University of Washington. Rowen is working with Geospiza to develop sequencing informatics for her chromosome-14 project. "They have a good understanding of our conceptual needs and they understand how sequencing works because of their backgrounds."

--Amy E. Nevala

Filed under

The Scan

Support for Moderna Booster

An FDA advisory committee supports authorizing a booster for Moderna's SARS-CoV-2 vaccine, CNN reports.

Testing at UK Lab Suspended

SARS-CoV-2 testing at a UK lab has been suspended following a number of false negative results.

J&J CSO to Step Down

The Wall Street Journal reports that Paul Stoffels will be stepping down as chief scientific officer at Johnson & Johnson by the end of the year.

Science Papers Present Proteo-Genomic Map of Human Health, Brain Tumor Target, Tool to Infer CNVs

In Science this week: gene-protein-disease map, epigenomic and transcriptomic approach highlights potential therapeutic target for gliomas, and more