Development of a Database Management System to Enable Rapid, Efficient Assay Design for Use in Detection and Diagnosis of Human Exposure to Biological

Period of Performance: 06/15/2008 - 06/15/2010

$765K

Phase 2 SBIR

Recipient Firm

CFD Research Corp.
701 McMillian Way NW Suite D
Huntsville, AL 35806
Principal Investigator

Abstract

Increases in amount and diversity of high-throughput data presents tremendous organizational and analysis challenges to researchers. Our objective in this effort is to address these challenges by designing and implementing a database management system (cipherDB) for the storage, management, analysis, and visualization of diverse biological data types. The Phase I design and implementation of cipherDB was established in close consultation with USAMRIID researchers. Successful completion of Phase I demonstrated cipherDB s ability to manage content, process data with flexible querying, and enable assay design using plague infected non-human primates as an example. The Phase II effort will build off of Phase I by expanding the scope and capability of cipherDB. Phase II will begin with improvements to the Data, Logic, and Presentation Tiers with the goal of maximizing the value of the resultant software to USAMRIID research efforts. Data Tier improvements include the addition of multiple Minimum Information About (MIA)-type data representations. Other additions include biological sample tracking and DNA microarray probe management to enable targeted array development. Logic Tier improvements include addition of data security and the capture of an analysis pipeline to enable automation and sharing of computations. Finally, Presentation Tier improvements include the creation of user home pages containing relevant data, analysis pipelines, and links to online databases. A suite of bioinformatics and systems biology tools will also be developed as part of the Phase II effort. Bioconductor will provide the basic analysis capability, while advanced systems biology and bioinformatics methods will be developed with the goal of objectively ranking the relative importance of specific genes/proteins within a complex biological network. Successful completion of the Phase II effort will generate a DBMS containing a critical set of analysis tools that will ultimately provide a rational basis for the design of diagnostic assays for human exposure to biological threat agents.