Register by Dec. 1 for workshop on National Microbial Pathogen Data Resource

released October 13, 2005

A tutorial on the National Microbial Pathogen Data Resource (NMPDR) will be held Dec. 14-15 at Argonne National Labs. The two-day course will cover basics such as searching for and finding a specific gene in a target organism and will move on to answering biological questions using NMPDR tools. Registration for the tutorial is open through Dec. 1 at http://www-fp.mcs.anl.gov/nmpdr/.

NMPDR is funded by the National Institute of Allergy and Infectious Disease (NIAID) as a Bioinformatics Resource Center (BRC) to support research in biodefense, emerging infectious diseases, and re-emerging pathogens. NMPDR provides infectious disease researchers with a single Web-based entry point to organism-related data necessary for advanced study and applications, such as the identification of potential targets for the development of vaccines, therapeutics, and diagnostics. NMPDR provides the advanced bioinformatics environment needed to identify genetic polymorphisms that correlate with phenotypes such as pathogenicity, drug resistance, morbidity, and infectivity. 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.

The first day of the tutorial is devoted to a thorough exploration of the NMPDR environment. The use of NMPDR to find and visualize a gene, the protein it encodes, and the context of the gene will be demonstrated. The NMPDR protein page presents both a tabular and graphic representation of the target gene and those genes found up- and down-stream on the chromosome.

Two powerful tools for comparative analysis of functional clustering that are linked as buttons on the NMPDR protein page will be demonstrated. If the target gene is known to be functionally clustered, the "Pins" button returns a graphic of gene clusters in homologous regions from many organisms, ordered phylogenetically. The "CL" button can be used to find homologs of the target gene that appear in functional clusters in the genomes of the other organisms, whether or not the target is functionally clustered in its own genome.

Also to be demonstrated are functional subsystems and the subsystem summaries annotated for core and supporting organisms. These summaries are informal metabolic reconstructions that are being fully developed by the NMPDR annotators.

Chromosome walking in the NMPDR environment using the Compare Regions tool will be demonstrated and compared to chromosome walking in the GBrowse environment.

The first day's demonstrations will wind up with the newest and most exciting NMPDR tool, which can find proteins that discriminate two sets of organisms or are common to a set of organisms. The tool could be used to compare virulent and avirulent strains, or pathogenic with nonpathogenic species.

Day two of the tutorial is devoted to case studies in which the NMPDR tools will be used to find answers to questions relevant to the research goals of tutorial participants.

NMPDR is a collaboration among researchers from the University of Chicago, the Fellowship for Interpretation of Genomes, Argonne National Laboratory, and NCSA.

 

Briefs Archive