SBIR-STTR Award

The objective of this proposal is to create an innovative bioinformatics system for the management and analysis of microarray data. It will be a new generation of informatics system that goes well beyond any system presently available. The system will not only allow users to track the generation of data with a flexible laboratory information management system (LIMS), but it will also allow users to track and manage the analysis of the data automatically with a pioneering analysis information management system (AIMS). The AIMS portion of the system interfaces with external bioinformatics tools and databases to allow users to process and interpret their data. The integration of LIMS and AIMS will produce dramatic new benefits to researchers in terms of improved research quality and decreased time to biological discovery. Existing microarray informatics systems are very incomplete solutions because they fail to address the entire process and fail to track and integrate critical experimental and analysis information. No existing solution provides as complete or as integrated a solution as system proposed here. Technologies developed for this proposal will also be extremely effective for the management and analysis of other biological, high throughput functional data besides microarrays.

Benefits:
Significant cost reductions for conducting and analyzing microarray experiments. Dramatic improvements in the speed for conducting microarray experiments and for analyzing and appropriately documenting results. Substantial new functionality to support collaboration and sharing of data and knowledge resulting from varied uses of microarray technologies.

Potential Commercial Applications:
New class of LIMS, AIMS, and LIMS-AIMS combination products for microarray, protein-protein interactions, and metabolic research markets.

The objective of this effort is to create an innovative bioinformatics platform for microarray data management and analysis. This platform will overcome the following limitations inherent in current microarray systems: (1) current systems typically do not address all types of array data, (2) current systems do not record the context of the samples, which hinders scientific and statistically relevant queries of the data, and (3) current systems do not track computational processes, which hampers data analysis. In order to take advantage of microarrays and manage the massive volume of data produced by them, scientists must have bioinformatics platforms like the one we are developing for this research. We propose to couple a highly sophisticated Laboratory Information Management System (LIMS) to a pioneering analysis information management system (AIMS) that executes computational processes and interfaces with external bioinformatics tools as well as databases. The integration of LIMS and AIMS will produce dramatic benefits for researchers throughout the DOD's Defense Technology Area Plan in Infectious Diseases of Military Importance by improving research quality and decreasing time to biological discovery. Some of the technologies used in this research were developed by 3rd Millennium for an Advanced Technology Program (ATP) grant (see Related Work section).The bioinformatics platform we are developing will benefit both the government and the private sector in drug development, toxicology studies, and disease treatment by improving research quality and decreasing time to biological discovery. For example, the platform will aid disease treatment by facilitating the development of gene expression molecular phenotype classifiers for disease states. These classifiers can be used to match drugs to the diseases against which they will be the most effective. The search engine we implemented in Phase 1 of the research and will develop further in Phase 2 can aid in the construction of such classifiers. The sophisticated engine can also help in drug development by identifying genes that are suitable drugable targets and have altered expression profiles in the disease state relative to the healthy state. Also, databases of expression profiles like the one we implemented in Phase 1 are already being used in drug toxicology studies to determine if candidate drugs have molecular phenotypes that are known to be toxic. Expression profile databases have also shown utility in identifying the function of genes that lack annotations. This is especially helpful for researchers who are working with organisms that have poorly annotated genomes like the disease causing agents Plasmodium falciparum (malaria) and Bacillus anthracis (anthrax). In order to realize the full potential of functional genomic technologies like microarrays, researchers throughout the DOD and private sector need bioinformatics platforms like the one we successfully developed for Phase 1 of the research and will develop further in Phase 2. Finally, technologies developed for this proposal will also be extremely effective for the management and analysis of other functional genomic data such as proteomic and metabolic data

Keywords:
lims microarray affymetrix bioinformatics functional genomics integration database