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ICSB, Virginia Tech, Sun Microsystems, Cedars-Sinai, Moffitt Cancer Center, BioSolution, Integromics, Integrated Genomics, Tsunamic Technologies, Astellas Pharma, Ingenuity, Bayer HealthCare, Biobase, IBM, Rensselaer Polytechnic Institute

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ICSB Issues Call for Proposals for ISMB/ECCB 2007 Industry Track
 
The International Society for Computational Biology has issued a call for proposals for a special “industry track” at the 2007 joint Intelligent Systems for Molecular Biology/European Conference on Computational Biology conference, to be held in Vienna, Austria, July 21-25.
 
The goal of the first-ever ISMB/ECCB industry track is to “bring together people from both academia and industry in a venue that highlights innovative applications and practical impact studies of life science informatics,” according to an ICSB statement.
 
The industry track will run in parallel with the regular ISMB tracks. Conference participants will get around 25 minutes to present their work, demonstrate software, and answer questions.
 
“The presentation should describe the business/scientific problem, the approach used, the current state of the project, an evaluation of the benefits, and future developments,” ICSB said. “The presentation will provide an opportunity to present your organization to the life science community and especially for younger scientists as they learn how life science informatics are used in your organization.”
 
ICSB stressed that industry track talks should focus on scientific content “and should not be used for sales pitches.”
 
Submissions are due on March 4 and should include a 250-word abstract and a PDF file with a draft version of presentation slides.
 
The editors will notify speakers of their acceptance by April 23, 2007.
 
Further information on submission guidelines is available here.
 

 
Virginia Tech Researchers Simulate DNA Nucleosome Flexibility
 
Researchers at Virginia Tech have used their System X supercomputer to simulate the full range of motions of a 147-base pair strand of DNA — the length of the nucleosome. 
 
The study, published in the December issue of the Biophysical Journal, indicates that DNA molecules are more flexible than previously thought.
 
Using 128 of System X’s 1,100 processors, the researchers simulated DNA “wiggling like a worm, showing greater flexibility than expected from the traditional view,” according to a Virginia Tech press release.
 
“The implication is that it may not cost much energy to bend the DNA — even to bend sharply,” said Alexey Onufriev, an assistant professor in the departments of computer science and physics at Virginia Tech and a co-author on the paper.
 
Onufriev developed an “implicit solvent” approach to address the computational challenges of water molecules in the simulation. The approach accounts for the role of water on average, but does not predict the movements of individual water molecules.
 
According to the paper’s abstract, a comparison of computed relative free energies shows that nucleosome folding “is associated with little, if any, energy cost relative to a smooth, ideal conformation of the DNA superhelix,” and isolated nucleosomal DNA was found to be “considerably more flexible than expected for a 147 bp stretch of DNA based on its canonical persistence length of 500 Å.”
 

 
Cedars-SinaiProteomicsCenter Installs Sun Cluster
 
Sun Microsystems said this week that the Spielberg Family Center for Applied Proteomics at Cedars-Sinai Medical Center has installed a cluster of 400 Sun Fire x64 servers along with Sun StorageTek solutions and Sun N1software.
 
The system more than quadruples Cedars-Sinai’s previous data-processing capacity while also decreasing cost and power consumption, Sun said in a statement.
 
Researchers at the center are using the system to analyze multiple terabytes of proteomic data from patient blood samples.
 
The center expects to generate four terabytes of data daily in 2007 and eight terabytes daily by 2008.
 

 
Moffitt Cancer Center Licenses Rosetta Resolver
 
Rosetta Biosoftware said this week that the H. Lee Moffitt Cancer Center and Research Institute has licensed the Rosetta Resolver gene expression analysis system.
 
The center will use Resolver to analyze data generated by the Institute's Total Cancer Care program with the goal of discovering cancer biomarkers.
 
Financial terms of the agreement were not disclosed.
 

 
BioSolution to Market Integromics' Microarray Software in France
 
Spanish bioinformatics developer Integromics this week said that BioSolution, a Paris-based biotech consulting company, will market its products in France.
 
Integromics’ software focuses on microarray management, including data analysis and data mining.
 
Financial terms of the deal were not disclosed.
 

 
Integrated Genomics Partners with Tsunamic Technologies to Develop Linux Clusters for Genome Annotation
 
Integrated Genomics and Tsunamic Technologies said this week that they have signed a contract to co-develop Linux clusters for large-scale genome annotation.
 
Integrated Genomics will implement its ERGO bioinformatics software on Tsunamic Technologies’ Linux clusters for “large-scale, high throughput genome annotation and comparative genomics” projects, the companies said.
 
Tsunamic, based in Orlando, Fla., offers pay-as-you-go cluster computing services through the Internet on an outsource basis.
 
John Elling, president of IG, said the partnership will allow IG researchers to “focus on refining and using our tools for genomic analysis rather than maintaining a computer cluster.”
 
Financial terms of the deal were not disclosed.
 

 
Astellas Pharma Licenses Ingenuity Pathway Analysis
 
Ingenuity Systems said this week that Astellas Pharma has licensed its Ingenuity Pathways Analysis software and Ingenuity Pathways Knowledge Base database.
 
Financial terms of the agreement were not provided.   
 

 
Bayer HealthCare Licenses Biobase’s BRENDA-AMENDA Database
 
Biobase said this week that Bayer HealthCare has licensed its BRENDA-AMENDA database for use in its target research group in Wuppertal, Germany.
 
BRENDA-AMENDA is an enhanced version of Biobase’s BRENDA enzyme database that includes a text-mining module called AMENDA.
 
According to Biobase, AMENDA expands BRENDA’s enzyme-related reference content by five-fold.
 
The BRENDA-AMENDA database includes information on more than 83,000 enzymes from 9,800 organisms.
 

 
IBM Donates $2.2M Blue Gene Computer to Rensselaer Polytechnic Institute
 
IBM is donating a Blue Gene supercomputer to Rensselaer Polytechnic Institute for use in biological simulations and computational research, Rensselaer said this week.
 
The $2.2 million Blue Gene system, which IBM awarded under its Shared University Research program, will support projects for developing biological simulation technologies, Rensselaer said.
 
The system will also be used for nanotechnology research.
 
The technology will be used for simulating medical devices in “virtual patients,” Rensselaer said, with potential applications in the design of drug-eluting stents, transdermal patches, and inhalers.
 
The Blue Gene system includes a single rack with 1,024 dual-processor compute nodes, 32 I/O nodes, a service node, a front-end node, and multiple terabytes of SAN-based disk storage.

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