BioIT Alliance Continues to Grow

Launched in 2006 with 15 members, the Microsoft-led BioIT Alliance has grown to 77 members and plans to expand its scope in a world in which the road to interoperability for users or vendors is not yet fully mapped.

At the recent Bio-IT World Conference, Rudy Potenzone, director of the BioIT Alliance and industry technology strategist for pharmaceuticals at Microsoft, said that one way the initiative plans to expand in the year ahead is by launching a SharePoint portal that will let users build and try out Web components.

As an example, Les Jordan, Microsoft's life science industry technology strategist, pointed out during a conference session that Thermo Fisher Scientific recently announced it was starting to enable results from its lab equipment to be output into the Open XML format.

With Open XML, he said, scientists can pull data off an instrument via a Web service and import it directly into the "scientist's favorite tool," Excel. It could then travel onto a high-performance computing cluster, while users can access the data in a portal where it can be viewed, searched, and shared. "It is sitting in an open standard and people can access it though a Web service," said Jordan. "This is going to allow people to innovate."

Richard LeDuc, co-director of Washington University School of Medicine's proteomics and mass-spectrometry core facility, voiced concerns about applying this idea in his facility because the conversion from Thermo's .RAW mass spectrometry files to Open XML files dramatically increases their size. He described himself as a heavy Microsoft user who also develops in the Microsoft environment.
Although he has not transformed files to Open XML, in the past he and his colleagues have written code to pull mass spectrometry data off instruments and to transform the proprietary .RAW binary files into XML. "They tend to explode, in my experience, on the order of threefold," he said.

—Vivien Marx

Bioinformatics Notes

Entelos has joined a Pfizer-funded consortium to identify drug targets. Entelos will work with the company and four universities to apply computational approaches to find new drug targets for diabetes and obesity. So far, Pfizer has given $14.4 million to fund the consortium for the next three years.

SGI announced that researchers at the University of Hawaii will use its SGI Altix 350 system to analyze the recently completed papaya genome. The International Papaya Genome Consortium is led by the University of Hawaii's Maqsudal Alam.

CLC Bio is partnering with Microsoft to integrate its bioinformatics tools with Microsoft technology platforms. So far, CLC has added support for Microsoft's SQL Server to its CLC Bioinformatics Database.

Datapoint

$5 million
Total amount the National Science Foundation plans to dole out in funding for bioinformatics proposals

Funded Grants

$376,717/FY2007
Daphnia Functional Genomics Resource
Grantee: Michael Pfrender, Utah State University
Began: July 1, 2007; Ends: May 31, 2011

This funding will support the development of a shared bioinformatics resource for researchers interested in studying gene-environment interactions using Daphnia as a model system. The project aims to build a SNP database to facilitate fine-scale mapping and establish the bioinformatics infrastructure to integrate genetic and phenotypic data from these panels with existing genomic data.

$255,645/FY2007
Re-engineering the MEGA Software Package
Grantee: Sudhir Kumar, Arizona State University
Began: Aug. 1, 2007; Ends: July 31, 2010

This grant will enable Kumar and his colleagues to tweak the source code of Molecular Evolutionary Genetics Analysis (MEGA), a popular genomics software tool. In order to upgrade MEGA, the researchers will augment its ability to interoperate with diverse data file formats, including integration of support for popular input/output file formats. They will also integrate 64-bit computing and SIMD technology to enhance its performance for large-scale analysis.