About the NMPDR
NMPDR is a Bioinformatics Resource Center that provides the advanced bioinformatics environment needed to identify genetic polymorphisms correlated with pathogenicity, drug resistance, morbidity, and infectivity. NMPDR is funded by the National Institute of Allergy and Infectious Disease (NIAID) to support research in biodefense, emerging infectious diseases, and re-emerging pathogens. NMPDR is both a central repository for a wide variety of scientific data on these pathogenic microorganisms and a platform for software tools that support investigator-driven data analysis, such as the identification of potential targets for the development of vaccines, therapeutics, and diagnostics.
NMPDR's goal is to support existing and newly developed techniques for comparative analysis to obtain a deeper understanding of the fundamental biology of a specific set of pathogenic organisms, and to promote efforts to counter the threats posed by these pathogens. The resource will integrate hundreds (and, eventually, thousands) of prokaryotic genomes with existing and newly generated functional data to support characterization and analysis of Category B food and water-borne diarrheagenic bacteria, Campylobacter jejuni, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnnificus, and Listeria monocytogenes. Also included are the enterotoxin B producing Staphylococcus aureus, as well as the re-emerging, antibiotic resistant pathogens Streptococcus pneumoniae and Streptococcus pyogenes (Group A Strep). NMPDR will provide the advanced bioinformatics environment needed to explicate the details of the physiology of the pathogens, to clarify the detailed variations that determine phenotype, and to develop consistent interpretations of functional data.
NMPDR employs a strategy of subsystems annotation to provide researchers with corrected functional annotations in a structured biological context. Nearly 500 distinct subsystems have been developed to describe central and secondary metabolism, complex structures, and virulence or other phenotypes. NMPDR includes all essentially complete, public genomes that provide a rich context for comparative analysis.
Collaborating on this project are researchers from the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the University of Illinois.
- The center is located at the Computation Institute at the University of Chicago and Argonne National Laboratory.
- A team from the Computation Institute provides the bioinformatics infrastructure and computational support for the center.
- FIG leads the functional analysis and annotation effort. FIG also works with members of the Computation Institute on the database and software infrastructure development, and integration and interoperability of data into and from the NMPDR.
- The NCSA at the University of Illinois in Urbana provides outreach and training services to the growing number of users on how to most effectively use the NMPDR.