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August 18, 2004 | During the judging for this year's Bio·IT World Best Practices awards, an intense debate erupted over how much clinical trial data should be available to researchers and sponsors before a trial is completed. Discussion was invigorating, and no clear consensus emerged. Generally speaking, we play by Vegas rules: What's said in the judging room stays in the judging room.

That said, here's my snapshot of 12 deserving entries, including three Honorable Recognition awards.

Guided by the Light 
Paris-based Laboratoire Kastler Brossel (École Normale Supérieure) won Honorable Recognition for Best Application of New Technology for its pioneering use of Quantum Dot imaging technology (see Feb. 2004 Bio·IT World, page 30). Hailed by Science as a "Top Ten Breakthrough" in 2003, quantum dots are nanoscale, semiconductor-based fluorescent probes that are brighter, longer lasting, and less toxic than fluorescent dyes.

Locus Pharmaceuticals described a 1,000-node computing cluster, proprietary algorithms, and a "virtual library" of 40,000 fragments to rapidly generate drug leads. Key to the approach is computing free energy for an entire protein-ligand interaction milieu. Locus says it can recapitulate 10 years of experimental chemistry in 10 days. The company's success in identifying five ligand-binding sites on p38 kinase, three of which yielded "active druggable ligand[s]," earned it Honorable Recognition for Best Platform.

The third Honorable Recognition went to Children's Memorial Hospital, Chicago, for Best Informatics Application. Eric Bremer developed neural network software, using SPSS tools, to classify brain tumors based on gene expression. Bremer has initiated FDA approval of a diagnostic test.

Among the entrants were many worthy examples of innovation and cooperation.

Final clinical study reports are notoriously difficult and labor intensive to prepare. Using SAS tools, biopharma XOMA developed its own clinical decision support system to speed the process and expand access. Company researchers now have "24x7 access to data and analyses during 75 percent of a trial's duration."

University of Texas Health Science Center tackled HIPAA compliance, implementing storage security appliances (CryptoStor from NeoScale) to protect sensitive data within its storage area network (SAN). Sensitive data can be stored centrally and more economically in encrypted form.

Part of the challenge in "electronifying" clinical trials is coaxing different applications to speak the same language. A P&G Pharmaceutical project that integrates interactive voice response (ClinPhone) data and electronic data capture (EDC) (Phase Forward) takes steps in that direction. Benefits include simplified data entry and passage of patient diary information directly into EDC case report forms.

The Scripps Research Institute used a new technique from Agilent to mask high-abundance proteins in serum analysis in its search for sepsis biomarkers. Scripps now has four promising biomarkers. Charles River Proteomic Services showcased its newly developed Web access to all phases of its lab process. Remote researchers can track project progress rapidly and in great depth. MDS Proteomics utilized TurboWorx software to capture unused cycles on its networked computers.

Johnson & Johnson Pharmaceutical Research & Development's microarray database grows by 1 million rows a day, mostly based on Affymetrix platforms. J&J developed a knowledge management system to permit its researchers to initiate, track, and analyze microarray experiments from around the world, using Microsoft SQL Server 8.

Using a proprietary algorithm, Compugen discovered that the natural occurrence of antisense RNA is far greater than thought. The work analyzed public and proprietary databases and identified 3,200 genes with NATs. IBM provided the hardware. Bioexpertise has developed a kind of online "Consumer Reports" for research journals (, with active forums including cardiovascular disease, diabetes, and rheumatology.

The 2004 Best Practices competition captured only a fraction of the exciting work being done. We look forward to honoring organizations of all sizes and stripes that are putting technology to work in pursuit of biomedical advances at next year's event. Good luck to all of this year's participants.* 

For reprints and/or copyright permission, please contact  Jay Mulhern, (781) 972-1359,