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By John Russell

December 15, 2002 | Gene Network Sciences (GNS) launched its new VisualCell tool with a flourish last month by winning Best of Show honors at BioITWorld Conference & Expo in San Diego just as the tool was made available.

VisualCell was one of four Best of Show recipients. Awards were presented in four product categories: informatics tools and data, IT infrastructure, knowledge management and collaboration software, and supporting applications. Winners were selected from three to four finalists in each category, out of a total of 50 Best of Show entries.

VisualCell, the standout product in informatics, is one of the few commercial "systems biology" tools to come to market so far. The goal of systems biology is to model biochemical pathways at a higher level and to permit researchers to use those models as predictive tools in drug discovery (see A Virtual Pharmacopeia, November Bio-IT World, page 58).

Creation of a formal DCL (diagrammatic cell language) to represent specific biochemical activity is VisualCell’s distinguishing feature. This language allows researchers to draw maps of complex biochemical interactions in much the same way electronics engineers use specific diagrammatic symbols to create drawings of complex electronic circuits. VisualCell diagrams can be automatically translated into computer code, which lets researchers run simulations to investigate what happens when various biochemical parameters are changed.

While GNS has no commercial customers yet, VisualCell has big ambitions. GNS has licensed the product to a number of prestigious research organizations, including MIT, the Institute for Systems Biology, and the Max Planck Institute. GNS also sells a library of annotated pathways to help researchers get started. And it offers Biomine, a gene expression analysis tool. Data from Biomine can be ported to VisualCell, which overlays on the pathway, showing where and with what intensity genes are expressed.

Other finalists in the informatics category included LION Bioscience for DiscoveryCenter and GeneticXchange for discoveryHub.

Best of Show winner in the IT infrastructure category was storage giant EMC Corp. for its Centera “Content Addressed Storage” product. Designed to provide fast access to data that seldom changes and featuring enhanced security tracking, Centera promises to help  work on HIPAA and 21CFR11 compliance.

EMC is working with a number of the informatics tools and data suppliers to create unique fingerprints that stay with the data as objects throughout its life. Two key partners include Documentum Inc. and Scientific Software Inc.
There were three other finalists in the IT infrastructure group, which had the most entries (18) of the four categories. IBM's powerful data center server, pSeries 690, was one. Avaki Corp.'s 2.5 grid management software was another. Avaki also introduced version 3.0, which has enhanced management tools, at the show. The third finalist was RLX Technologies for its RLX BLAST Cluster Solution.

SciTegic's Pipeline Pilot took top honors in knowledge management. Pipelining -- the automating of data-processing tasks for a multistep simulation or analysis -- has gained currency of late. It's seen as a way to free up researchers’ time. For example, a researcher could schedule and link the successive steps in an experiment, each conducted by a different application: data acquisition, data filtering, data mining, and results display. Moreover, Pipeline’s graphical interface, according to company officials, makes the design and creation of these task pipelines relatively painless.

Finalists in the knowledge management category include Accelrys Inc.'s Discovery Studio and a joint entry from Accenture and Tripos, “Integrated Computing Environment for High Performance Discovery.”

The top award for supporting applications went to the Chemical Computing Group (CCG) for MOE (the Molecular Operating Environment). In effect, MOE is a suite of life science applications that are tightly integrated because they share underlying code. Among the applications are molecular design, molecular modeling, and cheminformatics tools. CCG says the suite runs on most major Unix, Linux, and Windows platforms. Users also get access to application source code and an embedded programming language to permit customizing the applications provided or build entirely new ones.

Other finalists in supporting applications category were GNS's Biomine and Strand Genomics' Soochika. Both of these products are gene expression analysis tools, and both offer enhanced statistical analysis. The lack of rigorous statistical analysis of gene expression data has long been considered a problem because of unavoidable variation between expression data sets.

Soochika would certainly have won the award for most interesting name. Strand executives say Soochika means “needle” in Sanskrit. Finding scarce needles in huge haystacks is exactly what gene expression analysis is all about.

Best of Show Finalists and Winners

IT Infrastructure
· Avaki, 2.5 grid software
· EMC, Centera Content Addressed Storage System -- winner
· IBM, pSeries 690
· RLX Technologies, RLX BLAST Cluster Solution

Informatics Tools and Data 
· GeneticXchange, discoveryHub
· Gene Network Sciences, VisualCell -- winner
· LION Bioscience, DiscoveryCenter

Knowledge Management and Collaboration
· Accelrys, Discovery Studio
· Accenture/Tripos, Integrated Computing Environment for High Performance
· SciTegic, Pipeline Pilot v2.5 -- winner

Supporting Applications
· Chemical Computing Group, MOE (Molecular Operating Environment) -- winner
· Gene Network Sciences, Biomine
· Strand Genomics, Soochika

For reprints and/or copyright permission, please contact Angela Parsons, 781.972.5467.