NEW YORK--Vendors of bioinformatics tools and services have been seeing dollar signs since Craig Venter, founder of the Rockville, Md., Institute for Genomic Research (TIGR), announced plans to form a private company with Perkin Elmer Applied Biosystems and sequence the entire human genome within three years.
Despite ambiguities still surrounding the two-month old announcement, and regardless of the fact that the project promises to present new competition to software tools manufacturers, bioinformatics company executives who spoke with BioInform this month agreed that the news that complete human and Drosophila genome sequences will soon be made public can only be good for business.
"The more data that's publicly available the more business there is for us," explained Martin Sumner-Smith, whose firm, Base4 Bioinformatics in Mississauga, Ontario, provides systems integration services and custom database access to biotech companies. "What drives a lot of the business we have right now is biotech and pharmaceutical companies knowing that they're not taking maximum advantage of what's publicly available." Sumner-Smith said he expects data churned out by Venter's new company to generate "quite a bit" of business for Base4.
To be sure, Sumner-Smith and others admitted that their ability to speculate is constrained by how little is known yet about the data Venter will release. "I know that sequence is going to be released, but I don't know about sequence traces or what kind of assemblies are going to come out. Then there's the whole separate issue of annotation," said Cyrus Harmon, CEO of Neomorphic Software in Berkeley, Calif.
Sumner-Smith pointed out, "They're going to be releasing contiguous sequences that include many genes in a row. They may be in separate files and the only specific resource will refer to an annotation file. And one could conceive of ways the search may be against a raw sequence. Until we get a much better idea of how they'll be presenting the data, it's hard to say what our needs will be."
Peter Barrett, corporate vice-president of Perkin Elmer and executive vice-president of the new venture, told BioInform that the new company is "in discussions with customers to define exactly what the data will look like."
Hardware and software
Whatever the format, Sun Microsystems pharmaceutical marketing manager Gerry McAndrew predicted that the quarterly data releases Venter promised to make will instigate "a gold rush."
Sumner-Smith agreed: "These companies want to make sure they access everything that's in the public domain on a timely basis."
According to McAndrew, that's good news for Sun and other hardware suppliers, since more data will create increased demand for powerful servers. Companies that want to process the sequence information will "need a mountain of equipment," he contended.
"We'll probably have a terabyte or more of disk space filled within a year," Sumner-Smith said. "The Venter data won't force us to buy new equipment, but our typical clients--biotech companies--don't have big servers to do the various things that are necessary."
Harmon said he expects to "need more horsepower on the analysis side." But he added that he's excited about the opportunity to test Neomorphic's products with the increased dataload. "We've been focusing on high-throughput, scalable approaches from the beginning, so we think our tools will really shine," Harmon remarked.
As Venter gets operations at his new company up and running, he has said he will first sequence the fruitfly genome by next April.
Observed Harmon, "That means that by April we're going to have a volume of sequence in our database that we didn't think we would have for three years. It's great. It's an opportunity for us to prove that our systems will scale and handle that volume of data."
Thomas Marr, president of Boulder, Colo.-based bioinformatics software company Genomica, said his firm is equipped for whatever quantity of data Venter's group releases. "We've started scaling up our tools to handle what's coming out of the Sanger Centre and Washington University," he noted. Marr said data anticipated from the new company will make Genomica's products "more useful sooner."
"We're excited this will be in the public sector," remarked Charlene Son, Pangea Systems' director of product marketing. "We provide live datafeeds from sources such as Gen Bank so customers can have access to the most updated data securely within their firewalls and integrated with their own internal datasources."
Son predicted Pangea will gain increased business by using its current system to take advantage of the new data. "The main challenge is how to actually get value out of all that data once it's been created," she added.
Compete or partner
Bioinformatics firms aren't ignoring the fact that Venter's company will also present competition in the software tools business. Barrett said the company will definitely be developing software tools. "Everyone is focused on the sequencing. That's the launching point, but from that we'll extend."
But few in the business consider it a threat. Genomica's Marr remarked, "Sure, they'll present competition. But there's plenty of room."
Harmon said he's optimistic about the chance to collaborate. "Certainly they are a significant potential competitor, and with their acquisition of Molecular Informatics and PE Nelson they have their own efforts in bioinformatics. But I think it's more likely that there will be an opportunity for partnerships."
Barrett said though no discussions have taken place yet, the new company is "very open to partnerships where one plus one equals three."
For now, perhaps the biggest threat the Venter venture presents to the bioinformatics community is the drain it will place on its shallow pool of skilled professionals. Barrett told BioInform that several hundred applicants lined up outside TIGR's door for a job fair on a Saturday morning in late June. And a help wanted ad seeking "individuals with experience in software engineering, computational biology, bioinformatics, research and development, DNA sequencing, molecular genetics and management positions" drew 370 resumes.