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Expression Analysis, Tripos, United Devices, Virginia Bioinformatics Institute, AstraZeneca, Genaissance Pharmaceuticals, Jubilant Biosys, MathWorks, Inforsense, Oracle

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Expression Analysis Wraps up FDA ‘Mock Submission’

Expression Analysis, a Durham, NC-based microarray service provider, said last week that it has com-pleted the pilot phase of a “mock submission” of microarray data it is preparing for the US Food and Drug Administration. The FDA is sponsoring the collaborative project in an effort to develop guidelines for the format, content, and context for the future submission of microarray data as part of the drug approval process [BioInform 06-20-03].

Last week, Expression Analysis completed an XML-based submission of microarray gene expression data and associated results from a toxicology study conducted by Schering-Plough for a drug project it opted to discontinue.

The initial submission “contained information on laboratory and informatics infrastructure, RNA standards, biological and processing factors, data analysis methods, and data documentation,” said Steve McPhail, CEO of Expression Analysis. Next steps, he said, include “a series of detailed discussions with the FDA to refine these sections of the submission and, working closely with Schering-Plough, we will incorporate other toxicology results and the interpretation of the toxicogenomic data set.”

The company said previously that the project is scheduled for completion in October.


Tripos Taps UD as Grid Partner

Tripos and United Devices have entered into an agreement to grid-enable Tripos’ virtual screening applications to operate on UD’s grid computing platform, the companies said last week.

UD has similar agreements with Accelrys and computational chemistry startup Optive Research.

Tripos and UD will work together to port Tripos’ FlexX, FlexX-Pharm, and FlexE virtual screening programs, as well as the company’s Unity 3D chemical database search software, to UD’s Grid MP platform.


VBI To Serve as Bioinformatics Core for Mid-Atlantic Biodefense RCE

The Virginia Bioinformatics Institute at Virginia Tech said last week that it has been tapped as the genomics and bioinformatics core for a 15-university biodefense research collaboration.

The VBI will provide supercomputing capabilities and informatics software platforms to connect the numerous collaborators in the effort, part of a five-year, $350 million initiative that the National Institute of Allergy and Infectious Diseases announced Sept. 4 to establish eight Regional Centers of Excellence (RCEs) for Biodefense and Emerging Infectious Diseases at institutions across the country.

The VBI will support the mid-Atlantic RCE, which received $42 million of the total NIAID funding, and is led by the University of Maryland.

Researchers in the mid-Atlantic RCE team will use VBI’s PathPort (Pathogen Portal), an informatics platform designed to enable data gathering, storage, analysis and integration of pathogen-related genomics data.

The mid-Atlantic RCE includes Virginia Tech, the University of Maryland School of Medicine, Johns Hopkins University, the University of Pennsylvania, the University of Virginia, the Uniformed Services University of the Health Sciences, the University of Pittsburgh, George Washington University, Georgetown University, West Virginia University, Drexel University, the University of Vermont, the University of Missouri-Kansas City, the University of Maryland Biotechnology Institute, and Virginia Commonwealth University.


AstraZeneca Licenses STRENGTH Database from Genaissance

Genaissance Pharmaceuticals said last week that AstraZeneca had agreed to license information in its STRENGTH (Statin Response Examined by Genetic Haplotype Markers) database.

Under the terms of the agreement, AstraZeneca will receive non-exclusive access to the STRENGTH study database for research purposes for a limited period.

Genaissance said this deal is the second commercialization agreement related to the proprietary study data, which includes gene variation data on more than 400 patients treated with the statin class of drugs.


Jubilant Integrates PathArt with DecisionSite

Bangalore, India-based bioinformatics firm Jubilant Biosys said last week that it has integrated its PathArt database of signaling and metabolic pathways with Spotfire’s DecisionSite analytic software.

Jubilant said it has developed a Spotfire plug-in that will allow users to map data analyzed with DecisionSite directly onto PathArt’s more than 400 manually curated pathways.


MathWorks to Host MATLAB Bioinformatics Workshop

The MathWorks, the Natick, Mass.-based firm that markets the MATLAB numerical computation and visualization software, will be hosting free seminars for computational molecular biologists and other bioinformatics researchers performing sequence analysis and microarray data analysis.

Entitled, “Developing and Deploying Bioinformatics Applications with MATLAB,” the course will address ways users are using the software for bioinformatics research.

Seminars are scheduled for Sept. 18 in Boston and Oct. 7 in Princeton, NJ.

Further information is available at http://www.mathworks.com/company/seminars/index.shtml/seminar/338,0,0,0.


Inforsense integrates technology with oracle 10g database

Inforsense, of London, said it has integrated its Kensington Discovery Platform technology with Oracle’s new Database 10g (see story p.1), as part of its participation in the beta program for 10G.

This integration means that Inforsense’s Open Discovery Workflow technology will include Oracle data mining and text features.

Users of the software, the company said, will now be able to combine Kensington’s workflow engine and analytics, such as its data and text mining features, predictive modelling, visualization, and statistics, with Blast and other analytical functions of Oracle Data Mining.

The whole system is based on Oracle Database 10g’s grid computing capability.

 

Filed under

The Scan

Just Breathing

A new analysis suggests that most Mycobacterium tuberculosis is spread by aerosols from breathing, rather than by coughing, the New York Times reports.

Just Like This One

NPR reports that the World Health Organization has hired a South African biotech company to recreate mRNA vaccine for SARS-CoV-2 that is similar to the one developed by Moderna.

Slow Start

The Wall Street Journal reports that Biogen's Alzheimer's disease treatment had revenues for July through September that totaled $300,000.

Genome Research Papers on Cancer Chromatin, Splicing in the Thymus, Circular RNAs in Cancer

In Genome Research this week: analysis of bivalent chromatin sites, RBFOX splicing factors' role in thymic epithelial cells, and more.