BIOMEDICAL

Type of Work	Item	Explanation	Documentation
R&D	Gene model data management	This is Phase II of an SBIR project by Geospiza and The HDF Group, which did not receive funding. In Phase I, we developed a prototype called BioHDF that demonstrated the power of HDF5 for managing high volume, highly complex DNA sequencing data. In the Phase II research project, Geospiza and The HDF Group proposed to develop a portable, scalable, and adaptable file technology for genotyping software. From the proposal, this project includes following aims: 1. Extend the BioHDF data model to support polymorphism discovery and genotyping, and integrate diverse types of data from multiple technologies. 2. Build a complete application, accompanied by software tools and APIs, to support BioHDF use in the research community. 3. Build a prototype application for whole genome association studies based on linkage disequilibrium. 4. Research methods for incorporating BioHDF into enterprise applications for clinical research and diagnostics. The first products, based on BioHDF, will provide data models, APIs, software tools (I/O, algorithms), and a viewer based on HDFView, to support DNA polymorphism discovery and genotyping. Using BioHDF, researchers will be able perform resequencing-based SNP discovery, analyze genotyping data, and export data sets in formats ready for submission to key databases. As a programming environment, BioHDF will be easily extended to accept data from new genotyping platforms and format data for interchange with many databases. Additionally, BioHDF will be able to be used to support studying and performing linkage disequilibrium (LD) calculations in very large data sets like HapMap. BioHDF will be delivered to the research community as an open source technology. During Phase II and in Geospiza's follow on Phase III efforts, Geospiza will use BioHDF to deliver scalable software applications to support clinical research, diagnostics, and bio-manufacturing processes that utilize genetic data for personalized therapeutics. In short, Geospiza and The HDF Group expect to provide three deliverables to the research community at the conclusion of this project: 1. Complete prototype applications for polymorphism discovery and genotyping. 2. Software tools and frameworks for working with large data sets like HapMap. 3. Portable, scalable data storage technologies to support the next generation of instruments for genetic analysis.

Type of Work

Research & Development

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Item

Gene model data management

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Explanation

This is Phase II of an SBIR project by Geospiza and The HDF Group, which did not receive funding. In Phase I, we developed a prototype called BioHDF that demonstrated the power of HDF5 for managing high volume, highly complex DNA sequencing data. In the Phase II research project, Geospiza and The HDF Group proposed to develop a portable, scalable, and adaptable file technology for genotyping software. From the proposal, this project includes following aims:

• 1. Extend the BioHDF data model to support polymorphism discovery and genotyping, and integrate diverse types of data from multiple technologies.
• 2. Build a complete application, accompanied by software tools and APIs, to support BioHDF use in the research community.
• 3. Build a prototype application for whole genome association studies based on linkage disequilibrium.
• 4. Research methods for incorporating BioHDF into enterprise applications for clinical research and diagnostics.

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The first products, based on BioHDF, will provide data models, APIs, software tools (I/O, algorithms), and a viewer based on HDFView, to support DNA polymorphism discovery and genotyping. Using BioHDF, researchers will be able perform resequencing-based SNP discovery, analyze genotyping data, and export data sets in formats ready for submission to key databases. As a programming environment, BioHDF will be easily extended to accept data from new genotyping platforms and format data for interchange with many databases.

Additionally, BioHDF will be able to be used to support studying and performing linkage disequilibrium (LD) calculations in very large data sets like HapMap. BioHDF will be delivered to the research community as an open source technology. During Phase II and in Geospiza's follow on Phase III efforts, Geospiza will use BioHDF to deliver scalable software applications to support clinical research, diagnostics, and bio-manufacturing processes that utilize genetic data for personalized therapeutics.

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In short, Geospiza and The HDF Group expect to provide three deliverables to the research community at the conclusion of this project:
• 1. Complete prototype applications for polymorphism discovery and genotyping.
• 2. Software tools and frameworks for working with large data sets like HapMap.
• 3. Portable, scalable data storage technologies to support the next generation of instruments for genetic analysis.

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Documentation

Geospiza phase 2 proposal