Microbial Genome Annotation by

Undergraduates

Michael SierkSaint Vincent College

NIBLSE WorkshopApril 17, 2014

Context• Saint Vincent College

• Small Catholic liberal arts college

• Moderately Selective

• Biology, Biochemistry, Bioinformatics majors

• Biotechnology minor

JGI Microbial Annotation

• Joint Genome Institute Microbial Genome Annotation

• Cheryl Kerfeld, Seth Axen

• Institution picks genome

• Instructors assign genes to students

• Students fill out electronic notebook

• When finished, transfer information from notebook to annotation form

• Instructor rates quality for subsequent review by JGI staff

Implementation• BIN 218 Bioinformatics, Genomics, and

Proteomics

• Required for Bioinformatics major, Biotechnology minor

• Elective for Biology major, CS major

• Offered odd-numbered years in the Fall (2011, 2013)

• Typically ~ 10 students

• BL 215 Molecular Genetics Lab• Required for Bioinformatics major, Cell/Molecular Biology

major

• Offered every Fall (2011, 2012, 2013)

• Typically ~ 20 students

Benefits

• Students learn about gene annotation techniques, software, etc.

• Genuine annotation (not just an exercise)

• Potential for their work to be used in JGI database

• Relatively low overhead

Limitations• Technical difficulties (minor)

• Some of the modules are difficult for the students to understand

• Need more instruction/in-class time

• Easy genes vs. hard genes

• Planned expansion into Microbiology, Biochemistry, Cell Biology, General Biology has not occurred yet

• All voluntary, no external incentives (negative or positive)

• Faculty uncomfortable with the technology and/or unwilling/unable to adapt/modify their curricula

• Student annotations not used in IMG database?