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Walsh Chosen to Participate in Prestigious Bioinformatics Institute

What's New, 2011-12-21

Walsh to Participate in U.S. Department of Energy (DOE) Joint Genome Institute (JGI) Undergraduate Research in Microbial Genome Annotation


Walsh University one of 26 nationally chosen to participate


Walsh University has been accepted to participate in the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) Undergraduate Research Program in Microbial Genome Annotation to be held at the DOE Joint Genome Institute in Walnut Creek, CA, January 19-20, 2012.

Walsh was chosen to participate as one of 26 teams nationally from a full range of undergraduate institutions with varying ideas for incorporating bioinformatics into their courses. This collaboration between JGI, undergraduate educators and their students is a response to the call to reform undergraduate life sciences education through research experience.

Photo of Dr. Thomas Freeland"Walsh University was chosen because our application demonstrated the potential to enrich the curriculum with sequence-based research," said Dr. Tom Freeland, Walsh director of bioinformatics and professor of biology. "We were told that our approach has the potential to contribute to the national model for undergraduate research that is being collectively developed."


The "Interpret a Genome" Program provides students in colleges and universities with access to recently sequenced microbial genomes, such as those of organisms from little-known branches of the Tree of Life selected as part of the DOE JGI's Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The students analyze and annotate the genomes in the context of their own class work, gaining hands-on knowledge of genomics and bioinformatics.

The research experience provides students with a "real-world" opportunity to study complete sequences of microorganisms and make novel discoveries that enrich the scientific community as a whole. Ultimately, the program's goal is to allow students nationwide to annotate GEBA genomes while learning about genomics and bioinformatics.

The Program is overseen by DOE JGI Education head Cheryl Kerfeld, recipient of the 2011 American Society for Biochemistry and Molecular Biology (ASBMB) Award for Exemplary Contributions to Education. Kerfeld was recognized for "encouraging effective teaching and learning of biochemistry and molecular biology through her own teaching, leadership in education, writing, educational research, mentoring and public enlightenment."

As their annotation platform, students will use the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT), a wiki/Web portal fusion that lets them work with existing genome datasets and record their discoveries. The platform is the result of collaboration between DOE JGI's education program and faculty members from several universities around the country.

Aside from access to genome data and "virtually endless" research possibilities, IMG-ACT offers students and their teachers access to bioinformatics databases, instructor course management and student notebooks.

Since the Program launch in 2008, 4,662 students and 157 instructors from 83 institutions have used IMG-ACT. There will be 28 instructors from 16 institutions at the January 2012 workshop at the DOE JGI headquarters in Walnut Creek, Calif., bringing the total number of instructors to 175 and the total number of institutions to 99.

Additional faculty training is now supported by an NSF grant. IMG-ACT is in turn linked to other databases used in microbial genome annotation, including IMG/EDU, the educational version of the Integrated Microbial Genomes database that is widely used by researchers in genome biology.

A complementary metagenomics annotation tool, IMG-ACTM has also been developed by the DOE JGI Education Program and is currently being used by the first test group of instructors.

Supported by the Office of Biological and Environmental Research in the DOE Office of Science, the DOE JGI enables scientists from universities and national laboratories around the world to probe the hidden world of microbes and plants for innovative solutions to the nation's major challenges in energy, climate, and environment. Follow the DOE JGI on Twitter and Facebook.