Gladstone scientists announce new version of bioinformatics software program

A team of scientists at the J. David Gladstone Institutes has unveiled a new version of GenMAPP, a widely used software program designed to help biomedical scientists view and analyze genome-scale data sets in the context of biological pathways.

GenMAPP 2.0, short for Gene Map Annotator and Pathway Profiler, marks the first major revision of the program, which was developed and launched by Gladstone scientists in 2002. With the program having been freely available at www.GenMAPP.org to all researchers since its debut, it has now become a standard means of depicting and sharing biological data and pathway information.

As GenMAPP developer Bruce Conklin, MD, points out, a single genomics experiment can yield enough data to fill a large telephone book, and methods for organizing and analyzing the data are desperately needed.

"Genomic experiments can easily overwhelm a scientist with data," explained Conklin, an investigator at the Gladstone Institute of Cardiovascular Disease and UCSF associate professor of medicine, molecular and cellular pharmacology. "GenMAPP organizes the data by biological process, a scheme that most biologists understand, and allows us to find new connections that we would not have seen otherwise."

From its beginnings, GenMAPP has been designed for viewing and analyzing gene expression data on biological pathways and other groupings of genes. GenMAPP 2.0 incorporates a variety of new features, many of them suggested by users, including:

  • A flexible format that accepts many different gene ID systems from resources for many species, including human, Drosophila (fruit fly), mouse, rat, zebrafish, C. elegans (a microscopic roundworm), and S. cerevisiae (yeast).

  • Species-specific gene databases that show relationships between the various gene ID systems in the database. For example, genes on the MAPP (GenMAPP files that represent biological pathways or groupings of genes) may use a single comm

Contact: John Watson
University of California - San Francisco

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