Geospiza Awarded Grant from STTR to Test Feasibility of HDF5 Scientific File Format for Bioinformatics Applications
Geospiza, a leading developer of software systems for genomic core facilities, today announced that it has been awarded a $150,000 Phase I/6month STTR grant for testing the feasibility of HDF5 scientific file formatting for bioinformatics applications.
In this Phase I STTR project, Geospiza will collaborate with The HDF Group (THG) using their Hierarchical Data Format (HDF) from the National Center for Supercomputing Applications (NCSA). The team will test the feasibility of using HDF5 as a scientific file format and container for bioinformatics applications. The feasibility will be tested in applications focused on assessing genetic variation. The goals are to develop requirements and data models that support the computation and annotation phases of DNA sequencing using existing standards. The requirements and data model will then be used to create prototype applications for DNA sequencing-based SNP discovery. During the project, Geospiza and THG will work with the bioinformatics community for BioHDF adoption.
While Geospiza is primarily known for its Finch Suite software for managing, processing and delivering data to customers of genomic core facilities, the research arm of the company has also been engaged in reengineering algorithms for higher-scale application use as well as developing scalable data processing and management systems and cross-platform desktop software. Products from Geospiza’s research include rPhrap and FinchTV.
Geospiza’s chairman and CEO, Todd M. Smith, Ph.D. comments, “A challenge in today’s software systems lies in their data handling. Bioinformatics has some great technologies for computation, but the lack of interoperability and ability to randomly read and write data to the file system in a scalable way during computation forces application developers to spend a disproportionate amount of time writing file parsers, subdividing problems and creating redundant stores of data and information.” Smith adds, “This project is about attacking the problem at the data persistence layer and developing new technologies to meet these current and future challenges.”
About Small Business Technology Transfer (STTR)
The STTR program seeks to increase the participation of small businesses in Federal R&D and to increase private sector commercialization of technology developed through Federal R&D. The unique feature of the STTR program is the requirement for the small business concern applicant organization to formally collaborate with a research institution in Phase I and Phase II.
About The HDF Group (THG)
THG is a recently formed not-for-profit corporation whose mission is to sustain the HDF technologies and to support worldwide HDF user communities with production-level software and services. THG is a spin-off from the HDF group at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign ( http://hdf.ncsa.uiuc.edu ). THG’s mission is to develop, promote, deploy, and support open and free technologies that facilitate scientific data exchange, access, analysis, archiving and discovery. More information is available at www.hdfgroup.org .
About Geospiza
Founded in 1997, Geospiza combines deep IT and life science expertise to deliver genomics core labs a highly-efficient, fully-integrated, 21 CFR Part 11-compliant informatics platform for managing the production, analysis and communication of DNA sequencing and genotyping data and results. The company’s customers are primarily genomic core facilities and research laboratories in commercial, education, government and non-profit settings engaged in genomics, DNA sequencing, resequencing, genotyping, bio-marker discovery, pre-clinical diagnostics and discovery, forensics, EST analysis, expression analysis, and quantitative-PCR and proteomics projects. More information is available at www.geospiza.com .
