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Rosetta Biosoftware, Genedata, Bayer Schering, Cincinnati Genome Institute, Complete Genomics, Isilon, NIH, SAIC, Aureus Pharma, DNAStar, Lasergene, NCGR, SAS, JMP, DNAStar, Memorial Sloan-Kettering Cancer Center

Rosetta Biosoftware 'Business as Usual' Despite Merck's Restructuring
Merck’s Rosetta Biosoftware unit will be unaffected by the pharma giant’s recently announced restructuring, a Rosetta spokesperson told BioInform sister publication GenomeWeb Daily News this week.
In late October, Merck announced plans to lay off 7,200 employees worldwide and to close basic research sites in Tsukuba, Japan; Pomezia, Italy; and Seattle. The Seattle site is the home of Rosetta Inpharmatics, which Merck acquired in 2001 for $620 million. Since then, the Rosetta group has primarily served a research function for Merck, with the exception of the software business, which operated as a separate unit under the name of Rosetta Biosoftware.
Merck plans to move around 100 of the 300 Rosetta Inpharmatics employees to its research center in Boston, but Rosetta Biosoftware, which employs 60 people, plans on staying put, according to Kristen Stoops, senior director of marketing and alliances at Rosetta Biosoftware.
“It’s business as usual” for the software unit, Stoops said. “There has been no impact on our daily business operations, nor do we foresee any impact.”
Stoops said that there are no plans to relocate the software business, which will continue to operate “unaltered” despite the changes planned for the Rosetta Inpharmatics group.
Stoops acknowledged that there is a possibility that Merck may spin out Rosetta Biosoftware as an independent entity, but she noted that that option has “always been on the table” for the bioinformatics business. 

Genedata Expands Partnership with Bayer, Signs on U of Cincinnati
Genedata said this week that it has expanded its ongoing research informatics partnership with Bayer HealthCare to include all of Bayer Schering Pharma’s drug discovery research sites.
Separately, Genedata announced that the University of Cincinnati will use its data analysis software for high-throughput screening in its pharmaceutical studies program.
Genedata’s partnership with Bayer began in 1999 and was renewed in 2006. The Genedata collaboration includes providing and tailoring the Genedata’s Expressionist and Phylosopher platforms to support BSP’s research.
Phylosopher is a platform to integrate target and proprietary compound information, patent information, disease pathways, and experimental information. Expressionist is used for high-throughput processing and quality control of raw gene expression data as well as for statistical analysis to identify differentially expressed genes for target candidate identification, compound profiling, and mode of action studies.
As part of the partnership, Genedata will also provide professional services to support integration and to lend interfaces to existing research logistics infrastructure including laboratory technologies and related IT systems.
Under the collaborative agreement with the University of Cincinnati, the Drug Discovery Center at the university's Genome Research Institute will use Genedata's Screener software for high-throughput and high-content screening research projects.
The company said that the software includes assay data management and analysis tools that are independent of tools, technology, volume, or location.
The DDC is developing molecular probes for use in pharmaceutical and biotechnology applications.
Financial terms of the agreements were not released.

Complete Genomics Selects Isilon IQ for Storage
Next-generation sequencing developer Complete Genomics said this week that it is deploying more than 700 terabytes of Isilon IQ clustered storage to store genetic data and help power its DNA sequencing pipeline. No financial information was released.
Complete Genomics officials told BioInform last month that the company had 400 terabytes of disk storage at the time and that it plans to scale up to 5 petabytes of disk storage next year. By 2010, it expects to ramp up its storage capacity to 30 petabytes of storage [BioInform 10-10-08].
The company said in a statement this week that Isilon IQ has accelerated its research and development operations such as DNA sequencing, software development, and large-scale bioinformatics simulations, and has eliminated the requirement for a full-time storage administrator.
Additionally, Isilon IQ, featuring its OneFS operating system software, provides Complete Genomics' Linux clustered compute farm a centralized, near-line storage archive for access to its DNA sequencing data. Isilon IQ features N+3 and N+4 data protection.
Complete Genomics plans to offer human genome sequencing services for $5,000 by mid-2009. It expects to sequence 1,000 complete human genomes next year and 20,000 genomes in 2010. By the end of 2010, it expects to be able to sequence 200 genomes a day.
Bruce Martin, vice president of software at Complete Genomics, said in statement that the company’s sequencing service “requires enormous amounts of genetic data to be accessed, analyzed, and stored on an around-the-clock basis, making a highly scalable, high-performance and easy to use storage solution critical to our workflow.”
With Isilon IQ, he said, “we have unified our data onto a single, pay-as-you-grow storage repository to support our staggering data growth without requiring a full-time storage administrator."

NIH Awards SAIC up to $61M for Electronic Grant Administration
Science Applications International Corporation said this week that it has received a contract from the National Institutes of Health’s Office of Research Information Systems to provide software development support services to the electronic Research Administration.
The single-award contract, with a one-year base period of performance and four one-year options, has a total contract value of more than $61 million if all options are exercised.
The eRA systems provide information technology solutions and support for NIH’s grants administration functions with systems managing receipt, processing, review, award and monitoring of over $30 billion in grants awarded annually.

Aureus Pharma Joins European Consortium for Drug Cardiac Toxicity
Aureus Pharma said this week that it has joined a consortium of industrial and academic research teams in a European Commission-funded project entitled “preDiCT: Computational Prediction of Drug Cardiac Toxicity.”
The goal of the three-year preDiCT project is to develop models to predict the effects of drugs on the heart in order to better understand why many potential drug candidates fail during drug development due to adverse cardiotoxicity safety factors.
Aureus said it will use its Ion Channel/hERG knowledge databases and knowledge management tools to design, build, and populate a platform required for storing the experimental data. This platform will be used to build models as well as the framework for collecting the knowledge generated in the modeling studies.
In addition to Aureus Pharma, other participants in the consortium include F. Hoffmann-LaRoche, Fujitsu Laboratories of Europe, GlaxoSmithkline Research and Development, Novartis Pharma, University of Szeged, Universidad Politécnica de Valencia, and the Center for Advanced Studies Research & Development in Sardinia. The University of Oxford is the coordinator of the project.
The project is part of a larger European Commission linked to the Virtual Physiological Human Network of Excellence. More information related to preDiCT can be found here 

NCGR Using JMP's Visualization Software for Next-Gen Sequencing
The National Center for Genome Resources and SAS business unit JMP will co-develop software tools for next-generation sequencing data analysis, SAS said this week.  
NCGR researchers have been using the JMP Genomics software suite to analyze sequence data and have been offering advice about how to enhance the software, said Russ Wolfinger, director of scientific discovery and genomics at SAS. Wolfinger said that the “valuable suggestions for enhancements … will shape the software’s capabilities in future versions.”
Santa Fe, NM-based NCGR said that its researchers are using JMP Genomics in its research programs, including studies of schizophrenia and soybean genetics, under a license signed a year ago. Researchers there also use their own Alpheus software along with JMP Genomics visualization technology.
The NCGR center includes six Illumina Genome Analyzer II sequencers and it provides sequencing for both NCGR and for outside clients.
Financial terms of the agreement were not released.

DNAStar Extends Lasergene License with Memorial Sloan-Kettering
DNAStar said this week that it has extended its site license agreement with Memorial Sloan-Kettering Cancer Center for the Lasergene sequence analysis software.
The company did not release financial details.
Under the three-year agreement, the software will be available to all of the researchers at MSKCC’s New York City location.
The cancer hospital and research center first licensed the software, which can be used for assembly and analysis applications for conventional and next-generation sequencing programs, in 2000.

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