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3rd Millennium Goes Out on a LIMS


By John Russell

June 14, 2006 | Commercial LIMS systems have a bad reputation. Conventional wisdom is they are expensive and too rigid. At a panel* this spring, Andy Palmer, an informatics executive at Infinity Pharmaceuticals, labeled the lack of “standard, good-quality, third-party LIMS” as appalling, and his fellow panelists, mostly from Big Pharma, agreed.

At least one company, 3rd Millennium, hopes Palmer is right, at least about LIMS used for microarray research. This small, previously consulting-only company has just launched a commercial LIMS product, ARDAS, which was originally developed for the Department of Defense (DoD) using two SBIRs (Small Business Innovation Research) grants. While SBIR administrators hope technologies developed under its auspices reach the commercial market, it’s often the case they don’t.

The market will decide whether 3rd Millennium’s plunge into product sales is smart. Company president Ousama Shamma is betting that low-priced product, vetted by the DoD  (it won a 2005 Army quality award) and sold exclusively over the Web and by direct marketing techniques, can carve out a space in what has been a problematic market.

“This is a different business model from other companies where maybe you get money from VCs,” says Shamma. “This was all funded through the SBIR, around $2 million in total. We worked to make it a shrink-wrapped product and decided to price it very low almost like desktop even though it’s an enterprise application.”

To contain costs, 3rd Millennium relied heavily on open-source technologies such as R development language and BioConductor.org applications. ARDAS includes workflow support for two-color spotted arrays (RNA extraction, labeling, post processing, etc.), and the repository supports Affymetrix and two-color spotted data. The systems was first developed to support Walter Reed Army Institute’s microarray lab in Maryland and to permit DoD researchers worldwide to access the system using the Web. MIAME compliance is also supported.

When the DoD project began, there were few commercial LIMS focused on microarray processes. Quality control and data cleanup — tasks that are now de rigueur — tended to be tackled ad hoc, raising questions about data integrity and complicating cross-platform comparisons.

“We actually paid a lot of attention to [data integrity issues]. It’s kind of interesting to look at older data sets where people did not have those kinds of tools. In some instances, the quality of the data is very good, but in some cases you can see something that if the investigator had access to the tools at the time, I’m sure the investigator would have rerun some of the chips,” says Roland Carel, head of informatics.

Shamma says 3rd Millennium will divide its small full-time workforce of 10 and dedicate four to ARDAS development and support. “Consultants have often failed when they tried to do this because they did not separate the two efforts,” he says.

*Buyers Panel, Bio•IT World Life Sciences Conference + Expo in Boston, April 4, 2006.

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