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Bioinformatics Briefs: Mar 4, 2002


New PNAS Paper Criticizes Celera’s WGS Approach

Looks like the dust hasn’t quite settled on the disagreement between the Human Genome Project and Celera. In a paper in this week’s Proceedings of the National Academy of Sciences, Robert Waterston, Eric Lander, and John Sulston analyze whether Celera’s paper on its sequence of the human genome “provides a meaningful test of the whole-genome shotgun approach on a mammalian genome.”

Predictably, the authors determine that because Celera’s approach was so dependent on public data, its paper did not provide valid evidence that the WGS technique works. The authors stress that their analysis doesn’t address whether the WGS approach is lacking, but “merely that the Celera paper does not provide such evidence.”

Don’t count on this being the last word in this debate. Several Celera scientists, including Gene Myers and Mark Adams, have said since publishing the paper last year that the company is taking a closer look at its pure WGS data and is finding it to be valid without the inclusion of HGP data. An upcoming issue of PNAS will address “issues surrounding genome-sequencing strategies,” according to the journal, and will include two commentaries: one by Phil Green and another by Hamilton Smith, Mark Adams, Gene Myers, and Craig Venter.


Metaphorics to Improve Software with Syrrx


Metaphorics, a Mission Viejo, Calif.-based informatics company, said last week that it had entered a collaboration with San Diego-based structural proteomics company Syrrx.

The companies will work together to improve on Metaphorics’ DockIt small-molecule docking software. The companies expect to enhance the software’s ability to “predict the potential complementarity between ligands and proteins,” according to a statement.

Syrrx has been running DockIt on a 500-node Linux cluster for over a year and plans to expand this to 1,000 nodes by mid-2002. The company will contribute its experience in analyzing structural data to the collaboration, while Metaphorics will stick to the informatics side of the project.


LabBook Gains a Stronger Foothold in Japan


In two separate deals announced last week, LabBook of McLean Va., expanded its presence in the Japanese market.

Fujitsu licensed the company’s Genomic XML Browser, BSML converters, and eLabBook desktop electronic notebook for use in its internal development efforts in addition to integration services it supplies for its pharmaceutical clients.

Meanwhile, Itochu, a multinational diversified organization, agreed to distribute the Genomic XML Browser through several of its subsidiaries, including CRC Solutions, an IT and biotech contract research organization with a large data center in Japan.


AstraZeneca Taps Platform for Compute Farm Management


Platform Computing said last week that AstraZeneca would use Platform LSF to manage three heterogeneous large-scale compute farms within its Discovery Function.

In Alderley Park, Cheshire, UK, AstraZeneca’s Enabling Science and Technology department will put 130 Platform LSF licenses to work on a farm of 110 IBM Linux servers and 8 SGI IRIX servers. The company’s Blackley, UK, Discovery Information Systems department will run a cluster of 204 Compaq ES40 servers with over 200 Platform LSF licenses. In Molndal, Sweden, the AstraZeneca R&D site supports a SGI IRIX server farm for over 200 scientists.


OmniViz Collaborates with Affy


Visualization tool provider OmniViz of Maynard, Mass., is working with Affymetrix to integrate its software system with Affymetrix Analysis Data Model (AADM)-compliant databases.

After the project is completed, researchers using the OmniViz Gene Expression module will be able to analyze data from Affy’s GeneChip arrays along with other types of data, including sequence, textual, numerical, and categorical, the companies said last week.

BioDiscovery and Genops Enter Integration Partnership


BioDiscovery, based in Marina Del Ray, Calif., and Genops Bioinformatics of Vancouver, Canada, said last week that they had entered into a strategic collaboration to merge their microarray- and sequence-based analysis platforms.

Under the terms of the agreement, BioDiscovery’s GeneDirector, CloneTracker, ImaGene, and GeneSight data analysis products will be integrated with Genops’ Ngene sequence analysis platform.

Financial terms of the agreement were not disclosed.


SBI Uses Computational Approach to Predict HIV-1 Resistance


Structural Bioinformatics of San Diego said last week that it has successfully developed a computational method to predict HIV-1 resistance to protease inhibitor drugs in collaboration with scientists from Quest Diagnostics.

At the 9th Annual Conference on Retroviruses and Opportunistic Infections in Seattle, the company presented the results of a study that computationally modeled the structure of HIV protease complexed to clinically available protease inhibitors.

The researchers calculated the binding energy of each drug to the active site of the protease to determine the binding affinity of seven FDA-approved HIV protease inhibitor drugs. They were able to demonstrate with “a high degree of confidence” that the binding energy directly correlates to drug resistance measured with off-the-shelf phenotypic resistance assays.


ANNs Used to Diagnose Colon Cancer at University of Maryland


Researchers at the University of Maryland said they have successfully used artificial neural networks to differentiate and diagnose several types of colon tumors.

In a study to appear in the March issue of Gastroenterology, Stephen Meltzer, a professor of medicine at the University of Maryland School of Medicine, and colleagues describe how they trained an ANN to recognize the gene expression patterns of two types of colon cancer: those considered “sporadic,” which can often be removed without radical surgery, and those related to inflammatory bowel disease, which are generally treated by removing the entire colon.

The researchers used tissue samples from 27 patients to train the ANN.

Filed under

The Scan

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