MISSISSAUGA, Ont.--Martin Sumner-Smith would prefer the term "systems integrator," but his firm, Base4 Bioinformatics, might also be described as a bioinformatics consultant. Aside from customized databases, query tools, and a project management software package called PharMatrix, Base4's staff of two dozen computer engineers, biologists, pharmacologists, and chemists provide biotechnology and pharmaceutical companies with audits and services to help make the most of the data they generate.
"The academic view that bioinformatics is purely the assessment of new gene sequences and their function is a only a subset of what companies think of as bioinformatics," explained Sumner-Smith.
At the recent Intelligent Systems in Molecular Biology conference in Montreal, Sumner-Smith said bioinformatics specialists from industry told him that their concerns go beyond the new algorithms and gene sequencing methods that were discussed at the meeting. "The challenge for these companies is sharing information and knowledge among team members, no matter where it comes from," he told BioInform.
Helping biotech companies meet that challenge is where Base4 has found its niche in the bioinformatics market. "A lot of the so-called bioinformatics companies starting up now begin with just gene sequencing products. But they have to get involved in these other areas as well. It's tough to develop a software package that does everything. Most companies I know are buying combinations and putting them together in a pragmatic fashion," Sumner-Smith said.
Alan Hillyard, Base4's chief technology officer, contended that most people overestimate the role of biology in the informatics equation, while underestimating everything else. "There is a lot of fundamental application of information technology to this business. Biotech companies and even some pharmaceutical companies are pretty underdeveloped with respect to the application of information technology," he observed.
Added Sumner-Smith, "Companies are not just faced with how to take advantage of all these new gene sequences coming out. They need to deal with the fact that they're generating a lot more compounds, and they're doing a lot more screening than they ever did before. You have to take the holistic view."
That's the idea behind Base4's approach, even when clients aren't aware that such an assessment is what they need. Base4 typically gets new customers in one of two ways, according to Sumner-Smith: "Either we're hired by the information technology department for a specific project, or upper management calls us in to help track the organization's data."
"Usually the data are scattered on every hard drive in the company, totally unavailable to senior management," he remarked. "Manage ment says things like, we made a decisions six months ago and we're not sure what data we had at the time we made it, or why we made it," Sumner-Smith explained.
Base4's PharMatrix product can help a biotech better manage its diversified data. But Base4 doesn't just sell that product and walk away. Instead, the company will "almost always end up doing a systems review as we're engaged by a client," Hillyard said.
The systems review
During a systems audit of a typical biotech company, Base4 reviewers often find an eclectic mix of platforms. "Researchers have a mixture of PC's and Macs on their desktops. Scientists basically bought whatever they were familiar with, so there's a hodgepodge," Hillyard said.
He added, "If they have any kind of a workstation it's a Silicon Graphics machine, because the molecular modelers brought one in. Typically that's the first place where they start running into network difficulties, because they don't know how to talk between their desktop PC and the SGI Unix box," he explained.
Some small biotech companies lack even a network. Said Hillyard, "In a heterogeneous environment where you have Macs and PC's and Unix boxes, it's very difficult to make a network work well. That's usually where people start throwing up their hands and just put data onto floppy disks."
One Canadian company Base4 visited relied on manual data transmission to run a major sequencing effort, Hillyard recalled. "Two technicians were spending most of their time taking data from a sequencing machine on a floppy disk, converting it to a PC format, using a PC to enter it to a Unix machine, launching a search, then waiting for their result, seeing whether it was something interesting, and repeating that process over and over," he said.
Base4 networked the machines and automated the searches, freeing up the technicians to work at the bench.
"Our customers generally benefit just from a half hour's talk, even if they don't employ us any further. Just pointing out that these are not insurmountable hurdles is a help to them," Sumner-Smith said.
Just by initiating a discussion between information technology and scientific staffs, Base4 helped one customer in California. "While we were telling management about our review process, they brought the staff into the room to hear us. The IT people were saying, oh, we didn't know that was a problem, and the science people were saying, well, yes, it is," Sumner-Smith recalled.
After meeting with management, Base4 auditors sit down with each technical and administrative group at a client's site. "We're not interested in doing accounting or things like that, but, for example, chemists might want to automate the lab equipment ordering process, or secretaries typing proposals need to input data coming from applications programs that only the scientists use," Sumner-Smith explained.
Hillyard said customers also ask Base4 to recommend the best software package for their uses. "People have paid us to review all the candidate software packages out there. It's important that we're seen as being neutral. We're not reselling these packages."
Making diverse software work together is another area in which Base4 gets involved. "To that end we certainly have preferences for software," Hillyard acknowledged, "but we're pragmatic about it. People have software that they're running and using in their production department and you have to make whatever they've picked work together."
Four tiers of data
Sumner-Smith said that helping customers capture the knowledge they've generated through research is a growth area for his firm. He described a view of a four-tiered information system with hardware at the foundation. "The second layer is the data and the people who use it," he said. "We work very much in that layer, recommending what hardware customers should use to manage their data."
Sumner-Smith said the third layer--applications programs--is where most bioinformatics companies are focused. "We don't do much in that area other than recommending what packages to use," he said.
It's the top layer, which he called "the layer of knowledge where the results of analysis are captured," that Sumner-Smith sees holding new business opportunities for Base4.
Even major pharmaceuticals with more sophisticated infrastructures have trouble in knowledge management, Sumner-Smith claimed. "Their results are sitting in a hard drive or somebody's e-mail, not being shared among team members," he noted.
Or on several shelves full of zip cartridges, as was the case at a European biotech company Base4 saw. Sumner-Smith recalled, "They wanted us to develop a database so they would know what zip cartridge had what data on it." His audit quickly identified a better way to approach the problem.