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BioSequent Deploys ADINA Algorithm in Bioinformatics Integration Technology


Baltimore, Md.-based startup BioSequent may be small (with four full-time employees), and it may be young (the company was incorporated earlier this year), but co-founder and acting CEO Ed Addison is confident the company will be able to make its mark in the bioinformatics market through a combination of novel integration technology and IT expertise.

Addison, a partner with venture investing firm Infinity Venture Group and a part-time bioinformatics instructor at Johns Hopkins University’s Whiting School of Engineering, jumped into the life sciences IT venture about two years ago because he saw it as “the next market” after the Internet collapse, “although it’s a little bit rough right now,” he acknowledged. “We came in with the objective of applying smart search and data mining technology to bioinformatics, seeing that, if you look at the funding in the bioinformatics world, there’s been a lot of good biology done and not that much good IT done.”

With that goal in mind, and a combination of internal funding, state funding, and Small Business Innovation Research grants, Addison and his colleagues began developing a technology platform centered around the integration of biological data. Addison said the company is working in three main areas right now: middleware for searching disparate data sources, “knowledge-based sequence alignment” that uses annotation information as well as sequence data to improve on Blast, and a protein structure prediction system that merges the results from a number of different existing programs to determine function.

Addison stressed that BioSequent is still “very early stage,” and “it’s more of a contract research company with the intent to develop intellectual property and products.” In the future, he said, “it’s not yet clear whether we’re going to be a standalone company that grows with a product suite or whether we’re going to end up becoming a part of someone else. But right now, we’re a small group that’s doing good work in developing innovative algorithms to do integration.”

The core of BioSequent’s integration platform is an algorithm developed at Johns Hopkins’ Applied Physics Laboratory called ADINA (Architecture for Distributed Information Access). David Silberberg, senior computer scientist at the Hopkins APL, described the approach at a Cambridge Healthtech Institute conference in Baltimore in September [BioInform 09-29-03] . The system, originally developed for the Department of Defense and the National Imagery and Mapping Agency, uses a heuristics-based approach to automatically navigate distributed databases, and eliminates the wrappers that most middleware approaches require to access heterogeneous data sources. Recognizing that “this technology would be great for bioinformatics,” Addison said he volunteered the BioSequent staff to help Silberberg’s group migrate the technology to bioinformatics data, supported by a grant from Technology Development Corporation, Maryland’s technology-transfer assistance program. BioSequent is currently in discussions with Hopkins about a licensing agreement to turn it into a bioinformatics product, Addison said.

BioSequent also has a Phase I SBIR grant from the Department of Energy to commercialize its protein structure prediction software. Addison said the goal of this effort is to automate a process that many people are doing manually right now: “we’re integrating information from many different packages, and applying evidential reasoning calculus to come up with the best composite answer so that a user would only have to go to one place.”

As a survivor of the dot-com era — his first venture was a search engine company acquired by Excalibur Technologies in 1995 — Addison said the search engine software business and the bioinformatics market offer similar challenges and opportunities. For example, he said, “End users on the Internet get to use search engines for free, but if you’re a large corporation and you want to set up a server to search your private information, you’ve got to pay for that software. And I think the same is going to hold true here. There is a lot of free stuff out there for the university researchers and grad students, and people who work for pharmaceutical companies can use it, too, but they don’t like to go outside the firewall to search.”

Addison was quick to note a key difference between the two markets, however: “[Bioinformatics] is a limited market. It is not like search engines where everyone needs one … so getting a price point to make the company sustainable can be a challenge if you’re a pure product company.” With that in mind, Addison said that BioSequent plans to offer services as well as products, “because the number of customers is smaller and if you just throw products over the wall, you’re not going to make enough money to grow a company.”

Addison said that lessons learned from the Internet boom and bust will dictate the growth curve of the company, which will follow more of a biotech-style pattern than a software-style pattern. “Things don’t happen overnight in the biotech world,” he said. “You have to take a 20-year horizon; you can’t take a three-year horizon like a dot-com company.”

— BT

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