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NIH, TGen, Waters, University of Manchester, Spotfire, OmniViz, SGI, Organon, HP, GeneBio, Genedata

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NIH Seeks SBIR/STTR Applications for Data Integration

The National Institutes of Health last week issued two funding opportunity announcements - one for the Small Business Innovation Research program and another for the Small Business Technology Transfer program - entitled "Integration of Heterogeneous Data Sources."

NIH said that no funds have been specifically set aside for either program, and that the number of awards and the amount of funds provided for awards have not been predetermined.

The purpose of the FOAs is "to encourage small businesses to develop innovative software for addressing the integration of distributed cross-disciplinary data sources into coherent knowledge bases for biomedical research."

NIH notes that applications "are expected to describe at least one biomedical research problem that will benefit from the proposed tool or tool set, as well as to describe how the approach will scale when applied to additional data sources and/or to other biomedical problems." In addition, "a reasonable mechanism for maintenance and expansion of the software as well as integration with existing solutions should be carefully outlined."

Details of the SBIR FOA are available at http://grants.nih.gov/grants/guide/pa-files/PA-06-011.html, while the STTR announcement is at http://grants.nih.gov/grants/guide/pa-files/PA-06-010.html.


TGen Says Cancer Screensaver Program Identifies Two Therapeutic Compounds

The Translational Genomics Research Institute said last week that the Pancreatic Cancer Screensaver Lifesaver program, which has been running for five months [BioInform 04-25-05], has identified two compounds "that show promise against pancreatic cancer."

The Screensaver Lifesaver program is a peer-to-peer program that links together millions of PCs that run a screensaver application that assesses the interactions between small drug-like molecules and cancer-causing targets.

Program participants include the National Foundation for Cancer Research, Oxford University, the NFCR Center for Targeted Cancer Therapies at the University of Arizona in Tucson, and TGen.

The screensaver application, available at http://www.grid.org, provides each desktop computer with an initial bundle of 100 molecules and a model of a target protein. The program calculates the binding energy between the small molecules and the targets and sends the results back to a data center.

The pancreatic program has identified a total of 917 potential chemical hits, with two compounds in particular showing promise as potential lead molecules


Waters Reports Flat Q3 Sales for Informatics Business

Waters officials said last week that sales of its NuGenesis informatics products were flat in the third quarter, and "significantly lower" than expectations.

Total sales for the period ended Oct. 1 increased 3 percent to $273 million from $264.8 million year over year, Waters said.

The firm did not break out financial details for its informatics business, but Douglas Berthiaume, chairman, president and CEO, said in a conference call that receipts from the NuGenesis product line, which Waters acquired last February [BioInform 020-2-04], were "pretty flat from quarter to quarter over the last four quarters, but that's significantly lower than our expectations for this business."

Berthiaume said that Waters expected large pharmaceutical companies "would be moving aggressively to take advantage of the data-management capabilities [of the Nugenesis SDMS system]. We thought they'd be under greater regulatory pressure to do it. What we're finding is that in this climate, they are apparently finding that while you still get the salute that, 'Yeah, we need to do this. It's absolutely in our future. Yes, we've got old, unreliable data management systems and we need to improve on it,' but when it comes to making an investment in a brand new area for them, this climate is one of the most difficult to sell that kind of product into."


U of Manchester Awarded $3.4M for Middleware Institute, MyGrid Development

The University of Manchester said last week that it has been awarded £1.9 million ($3.4 million) to create the Open Middleware Infrastructure Institute-UK (OMII-UK), with the Universities of Edinburgh and Southampton.

The OMII-UK received total funding of £6 million from the UK's Engineering and Physical Sciences Research Council, and will be chaired by Carole Goble from the University of Manchester's School of Computer Science.

The center will develop middleware for the UK's e-science program, and the University of Manchester will focus on further development of the myGrid project, which kicked off in 2001 and has been targeted initially toward the bioinformatics community.


Erasmus University Medical Center to Use Spotfire DecisionSite …

The Erasmus University Medical Center, based in Rotterdam, the Netherlands, said last week that it has entered into a three-year bioinformatics collaboration with Spotfire.

Under the terms of the agreement, Spotfire's DecisionSite analytics software will be available to researchers and students at the medical center.

Erasmus MC and Spotfire said they plan to collaborate on the development of analytic tools for biomarker identification and pathway visualization, and will work together to integrate DecisionSite with other data sources, such as Ensembl from the European Bioinformatics Institute.

The organizations also intend to jointly "investigate the deployment of visualization methods in clinical research & diagnostics - especially where visual analytics can be used for personalized treatment of patients."

Financial terms of the agreement were not provided.


… And Expands Partnership with OmniViz

Erasmus MC announced separately last week that it had expanded an ongoing partnership with visualization software firm OmniViz.

The multi-year extension "will provide access to OmniViz capabilities across the institution," Erasmus MC said in a statement.

The ability of the OmniViz visualization methods "for dealing with very large volumes of data of all types, including full text documents, provides a critical capability for our research that is not otherwise met," said Peter van der Spek, the head the bioinformatics department at Erasmus MC, in a statement.

Financial terms of the agreement were not disclosed.


SGI Wins HPC Deployment Deals with NCI, Organon

Silicon Graphics said last week that the National Cancer Institute's Advanced Biomedical Computing Center in Frederick, Md., has purchased "a broad range" of SGI high-performance computing, visualization, and data storage systems for biomedical computing applications.

Separately, SGI said that Organon International, a business unit of Akzo Nobel, had upgraded the SGI hardware for its primary research center in Oss, the Netherlands.

The ABCC purchased an Altix 3700 supercomputer with 256 Intel Itanium 2 processors running Linux. The center also purchased a 50 TB SGI InfiniteStorage Total Performance 9700 RAID storage array.

The ABCC will also convert an existing 64-processor Altix server to a 64-processor Silicon Graphics Prism, which SGI said will be "the world's largest Prism system of its kind anywhere." ABCC has also purchased an SGI Reality Center - an immersive visualization environment that is expected to enable "a high level of interactivity with very large visual data sets, such as large molecules."

Organon, meanwhile, replaced two older SGI servers with an Altix 350 system with 32 GB of memory on 16 Intel Itanium 2 processors running Linux, and a 16-processor Origin 3800 system running the SGI's Irix operating system.

Organon also has an SGI CXFS SAN storage system that provides access to five file systems located on four SGI InfiniteStorage TP9100 disk arrays and to 8 TB of archived data on a StorageTek L-180 tape library with four LTO gen-2 tape drives.


HP Cluster Powers Malaysia's MGRC

Hewlett-Packard last week provided details about the cluster it has deployed to support the Malaysian Genomics Resource Center, which launched in July [BioInform 07-04-05].

HP said it has installed an Itanium 2-based HP Integrity rx4640 cluster server with 64 GB of RAM for the MGRC, which serves as an application service provider for bioinformatics researchers and runs SynaBase, a structured network database system developed by Synamatix .

MGRC said in a statement that it currently supports 70 active users worldwide.


GeneBio and Genedata Integrate Proteomics Software

Geneva Bioinformatics and Genedata said last week that they will integrate Genedata's Expressionist software with GeneBio's Melanie/ImageMaster 2D Platinum system for 2D gel analysis.

The companies also plan to integrate Expressionist with GeneBio's Phenyx mass spectrometry data analysis platform.

Filed under

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.