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Microbial Genome Annotation by Undergraduates

Microbial Genome Annotation by Undergraduates. Michael Sierk Saint Vincent College NIBLSE Workshop April 17, 2014. Context. Saint Vincent College Small Catholic liberal arts college Moderately Selective Biology, Biochemistry, Bioinformatics majors Biotechnology minor.

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Microbial Genome Annotation by Undergraduates

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  1. Microbial Genome Annotation by Undergraduates • Michael Sierk • Saint Vincent College • NIBLSE Workshop • April 17, 2014

  2. Context • Saint Vincent College • Small Catholic liberal arts college • Moderately Selective • Biology, Biochemistry, Bioinformatics majors • Biotechnology minor

  3. 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

  4. 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

  5. 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

  6. 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?

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