University of California
The JGI will be holding the JGI Genomics and Bioinformatics for Undergraduate Educators Workshop in conjunction with the JGI User Meeting. The workshop will take place March 23-26, 2013 at the JGI.
The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “interpret” bacterial genomes, such as those sequenced as part of the GEBA project, for analysis. This “Interpret a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. Genomic analysis of these organisms can provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, use gene ortholog neighborhoods for comparative genomics, and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.
Essentially, the goal of JGI’s Microbial Genome Analysis Program is to support the use of annotation to teach the curricular standards in new ways. For example, in biochemistry courses students can examine and annotate fundamental metabolic pathways, whereas in microbiology, pathways, structures, and systems characteristics of the organism’s lifestyle will be traced. Novel genes and pathways can be discovered by examining clusters of hypothetical proteins in a comparative genomics context (that will include phylogenetic profiling and ecological considerations), perhaps in an undergraduate course dedicated to bioinformatics. All bacterial genomes are full of novelties; moreover, the GEBA organisms are relatively unusual and from poorly investigated parts of the tree of life, so the likelihood of exciting discoveries and interesting variations on the classical pathways is high. The JGI believes that involving students in annotation in a calibrated, stepwise way will provide a new research-based approach to teaching fundamental concepts in the life science curriculum.
Go to the "Interpret a GEBA Genome for Education" page to view information on the GEBA genomes currently available for interpretation.
The long-term goal of the JGI’s Education program is to build on genome analysis and gene annotation with bacterial characterization and functional genomics, including both insertional mutagenesis and protein overexpression with subsequent biochemical and biophysical characterization.