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Reasons for Optimism

By John Russell

Aug 15, 2005 | Reading through the 33 submissions to the 2005 Bio-IT World Best Practices Awards Program provides plenty of reasons for optimism. One entry detailed the deployment of a giant LIMS that is a marvel of automated efficiency. Another described a system of hieroglyphic-like representations of proteins that is both information-rich and visually arresting. A few entries featured clinical trial management tools, including one built cleverly with off-the-shelf software. In fact, solving data management bottlenecks was a major theme this year. Following are a few highlights from the competition.

The J. Craig Venter Institute’s Joint Technology Center developed the mother of all LIMS for its giant sequencing factory. It provides bar-coded tracking of users, reagents, and material transfers in all operations — DNA extraction, library construction, and sequencing — and imposes process control and chain-of-custody requirements. Developed for $2 million, “J-LIMS” paid for itself in nine months and is busily sequencing DNA samples arriving from Venter’s round-the-world voyage as well as other projects. We were so impressed with its comprehensive precision that we gave it one of only two Editors’ Choice awards. Oracle is the underlying database. Symbol provides wireless PDAs for tracking operations. The center operates 24/7, can handle 80 million sequence reads per lane per year, and seems eerily empty while at work.

San Francisco General Hospital (SFGH) Core Immunology Lab, one of 78 such labs supported by NIH, described its efforts to improve data management. Sample receiving and processing were efficient, but analytical output was still done by cutting and pasting into Microsoft Excel. SFGH developed a new Flow Data Management System that has cut costs, improved accuracy, and enabled researchers worldwide to share data. Biotrue developed the underlying technology.

An award for the best name should go to Celera Genomics’ entry — “GlassHopper” data management platform, developed with help from Discovery Innovations (recently acquired by Entelos). Celera reports an 85-percent reduction in support required for its Protein Therapeutics Lab. The legacy system was inflexible and cumbersome (100 different screens and data-entry fields). GlassHopper will save 1,000 person-hours in the first year, says Celera.

Schering-Plough Research Institute, active in many disease areas, created the Analytic Discovery Portal to speed researcher access to its experimental capabilities and large data repository. Insightful provided much of the analysis technology. Oracle and Sybase data warehouses are also used.

Higher Standards
Michael Reich, Jill Mesirov, and fellow computational biologists at the Broad Institute of Harvard and MIT created an open-source software platform for integrative genomics that now has more than 1,000 registered users in 500 organizations. First released in January 2004, GenePattern hosts a variety of tools and manages their interactions. It’s a simple matter to add new tools using Web-based forms, without writing additional code. A pipeline environment allows users to chain analysis tasks into complex analytic workflows and to share those workflows. For their efforts and impressive result, we awarded them the second Editors’ Choice award.

Reducing paperwork in clinical trials is an ongoing effort. Working with Medidata Solutions, Janssen Pharmaceutica (a division of Johnson & Johnson) took a step forward, going paperless in two separate clinical trials at 230 sites. Janssen expects to lock its data four weeks earlier than with paper. The Department of Veterans Affairs entered another clinical trial solution. A Boston-based team created a portal-based system with off-the-shelf software (Microsoft Sharepoint Server), XML, and Web services. It’s 21 CFR 11-compliant, costs a fraction of commercial products, and has been distributed to 115 Veterans Administration hospitals.

After the 2005 winners were announced, a short e-mail from an examiner with the Kansas Award for Excellence program appeared in my inbox. He wondered what standards we use in judging the Bio-IT World Best Practices Awards. Kansas, he said, uses the stringent Malcolm Baldridge National Quality Award criteria. Could we share?

Wow. We’re hardly in the Baldridge criteria league, but working steadily to improve our Best Practices program. Maybe he has advice for us.

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