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Reflections on Good Practices

By Kevin Davies

July 29, 2010 | First Base | One of the undoubted highlights of our professional calendar is the second night of our annual Bio-IT World Conference & Expo, when we host a gala dinner for the announcement and presentation of our Best Practices Awards (see pages 16-28). The winners are profiled elsewhere in this issue, but it is important to note that our judges’ decisions were always hard, in some cases contentious even, and it would be a shame to dismiss the dozens of worthy entries merely to champion the nine winners.

Basic Research and Discovery: Working with JMP Genomics, Greg Gibson’s laboratory at the Georgia Institute of Technology is developing a high-throughput workflow to study “geographical genomics,” or the genetics of gene expression in global populations, with some impressive peer-reviewed publications already. Genstruct, a previous winner, impressed again with a causal network model of a liver cancer in a mouse model, in conjunction with Pfizer. And Sigma’s partnership with Ingenuity to create a free web-based biological search portal had its admirers.

Knowledge Management: Undoubtedly the most dynamic category, this spurred four awards in all. Among those edged out was Biovista, which is developing a very promising literature-based discovery platform for drug repositioning purposes. The judges were also impressed with HP’s ongoing work with the M.D. Anderson Cancer Center in Houston in building a Research Station platform to integrate genomic, transcriptomic and proteomic data. And Tessella presented CrysIS, an X-ray crystallography workflow tool now in worldwide deployment among drug design chemists across AstraZeneca.

In Personal and Translational Medicine, Merck followed up its 2008 Best Practice Award with phase two of its collaboration with the Moffitt Cancer Center, namely the establishment of a “data usability environment” to conduct hypothesis-driven research without the need of IT professionals. Merck also contributed a clinical imaging system being developed with IBM called i-SCORE, to improve and expedite the transfer of patient image files.

The IT & Informatics category was particularly strong. Convey Computer nominated a team at UCSD, for InsPecT, a fast database search tool for post-transitional modified mass spectrometry spectra. The Translational Genomics Research Institute (TGen) has developed the BIOMAP repository for the Integrated Biobank of Luxembourg.

On the High-Performance Computing side, there were strong entries nominated by companies such as Cycle Computing (Purdue), DataDirect Networks (Cornell), FalconStor Software (Baylor College of Medicine), Isilon Systems (Oklahoma Medical Research Foundation) and Panasas (Uppsala University). TGen also described its experiences building its next-gen data processing pipeline.

The Clinical Trials and Research category was populated with many successful vendor/pharma partnerships, ranging from dashboards and electronic data capture tools to a graphical user interface for trial designs.

As always, we thank everyone who participated in the 2010 competition, and not just the folks who are deservedly spotlighted elsewhere in this issue. We encourage everyone working on bold, imaginative solutions for managing research and data to consider entering their story when we open the gates for the 2011 competition in a few months’ time.

September Special

The next issue of Bio•IT World (September/October) will feature a special report on the march to the $1,000 genome. It will include reports and interviews on many facets of the next-generation sequencing industry, from a preview of third-generation platforms to current-generation software tools, as well as profiles of some key people in the field. It will also coincide with the publication of my new book, The $1,000 Genome, published by Free Press, which has been gestating over the past three years.

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