HPCwire: Geospiza and The HDF Group Awarded Grant

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March 17, 2009

Geospiza and The HDF Group Awarded Grant

Core Genomics data analysis tools will be delivered to the research community as open source technology

SAN DIEGO, March 17 -- Geospiza, Inc., the market leading developer of genetic analysis software, and The HDF Group today announced their collaboration to develop scalable bioinformatics technologies to support multiple Next Generation Sequencing applications such as Digital Gene Expression, Small RNA Analysis, Copy Number Variation and Resequencing based on HDF5 (Hierarchical Data Format -- http://www.hdfgroup.org), called "BioHDF", through a Phase II STTR grant awarded by the National Human Genome Research Institute.

Geospiza and The HDF Group are combining their expertise in genetic analysis and high-performance, scalable scientific data technologies to address data management issues that must be overcome to realize the full potential of present and future generation DNA sequencing platforms. Through this effort new data organization, storage, and access technologies will be created to reduce space requirements, while at the same time facilitate computational access to the data to support high performance computing.

This collaboration builds on Geospiza's commitment to work with the scientific and open source community to solve challenging issues related to scalable and cost effective genetic analysis. Geospiza's software, GeneSifter integrates many open source technologies like mapreads and MAQ as well as the R-statistical package to provide best-of-breed, peer-reviewed solutions to customers.

"We are looking forward to continuing our work with The HDF Group to find new ways to address the data analysis and data management challenges created by Next Gen Sequencing," said Todd Smith, founder and chief scientific officer of Geospiza. "Widespread adoption of Next Gen sequencing is being hindered because current bioinformatics approaches to working with these data simply do not scale. While Geospiza's hosted computing model solves many of the basic workflow issues faced by current desktop applications, more complex challenges arise when multiple analyses need to be performed. It is clear that 2nd and 3rd generation sequencing technologies will continue to push the limits of computing technology -- BioHDF will give us the needed foundation to rapidly provide innovative solutions to our customers and to the community as new opportunities to advance science emerge."

"The HDF Group is thrilled that the NIH has funded us to work with Geospiza on the data challenges posed by Next Gen Sequencing. Hundreds of applications, from flight testing to global climate research, already use the HDF data formats and software infrastructure to manage and access high volume, complex data," stated Mike Folk, president of The HDF Group. "Geospiza has been visionary on seeing how data intensive genomics applications can benefit from technologies like HDF that are designed to work with the specific features and attributes of scientific data."

Folk continued, "BioHDF will be a new face on top of the HDF infrastructure, making it seamless and easy to use by the bioinformatics community. Under the hood, we will extend and tune HDF to address unique challenges of genomic data, such as organizing and accessing tens of millions of sequences in complex workflows, and capturing the complex interrelationships among the myriad layers of data and information involved in even the simplest studies."

About Geospiza

Designed by biologists, Geospiza's products are configured to reflect best practices and to work out-of-the-box, so that researchers can focus on their discoveries. Used by researchers, laboratories and core facilities in universities, government, biotechnology, and pharmaceutical companies, Geospiza's software systems have established an international reputation for usability and performance since 1997. You can find more information on Geospiza and its products at www.geospiza.com.

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Source: Geospiza

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