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Undergraduate Genomics in a Research University Environment

This course offers a comprehensive view of the work and research conducted at a Genome Center in a research university. Students gain theoretical knowledge, practical training, and technical job skills in genomic science. The collaborative effort between the JGI and UC Merced provides expert instructors and training for a diverse workforce.

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Undergraduate Genomics in a Research University Environment

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  1. Undergraduate Genomics in a Research University Environment A Collaborative Effort between the JGI and UC Merced M. Pilar Francino DOE Joint Genome Institute Miriam Barlow and Mónica Medina University of California, Merced

  2. Up-to-date Genome Biology course giving a broad view of the work and research that goes on at a Genome Center Theoretical knowledge  Genomic Science + Practical training  Technical job

  3. A Collaborative Effort between a Genome center and a Research University UC Merced  Expertise of instructors JGI  Training of a diverse and well qualified workforce

  4. Spring semester 2007 11 undergraduate students (mostly upper division) & 3 graduate students

  5. CONCEPT  Classes and labs follow the implementation of a genome project from beginning to end Groups of students work on different small projects that illustrate a range of topics and methodologies in genome science

  6. Groups of 2 or 3 students 5 projects  16S rRNA environmental library of coral reef microbes  ESTs of anemone  ESTs of rockfish  Mitochondrial genomes of snails  Antibiotic resistance plasmids

  7. Conceptual knowledge Hands on computational skills Hands on wet lab skills • Prokaryotic evolution • Eukaryotic evolution • (plants, animals, protists, • organelles) • Metagenomics • Transcriptomics • Proteomics • Comparative Genomics • Template preparation • Library construction • Sequencing technologies (old and new) • • Genome assembly (i.e.Phred, phrap, consed) • Sequence comparison (i.e. Blast, clustal, ARB) • Genome comparison (i.e. Vista, IMG, Phigs)

  8. • 19 JGI researchers from all programs and departments lectured or organized laboratory sessions on their topics of expertise. Laboratory sessions followed the protocols in use at the JGI • 4 invited speakers from other institutions (Lawrence Berkeley National Lab, Pacific Northwest National Lab, Oakland Children’s Hospital) • 2 professors (Monica Medina and Miriam Barlow) and 1 TA (Shinichi Sunagawa) from UC Merced INSTRUCTORS

  9. MINI-JAMBOREE Genome annotation workshop at JGI + JGI Tour Organized by JGI Informatics Department (Annotation Group, Igor Grigoriev)

  10. INFRASTRUCTURE  Classrooms for wet labs and computer labs  UNIX server set up at Merced mirroring the computer system at the JGI  All bioinformatics software installed 2 weeks in advance. Test runs with sample files.  Life video-conferencing to the JGI

  11. ASSESSMENT 3 mid-term examinations students presented their projects in the last sessions of the course written reports

  12. FEEDBACK individual speaker evaluation forms final course evaluation forms + initial survey for next year

  13. ACKNOWLEDGEMENTS JGI  Production Department Susan Lucas, Tijana Glavina-DelRio  Project Management Kerry Barry  Informatics Department Igor Grigoriev and Astrid Terry  Administrative Services  Jennifer Kuehl  David Gilbert - JGI Outreach  Eddy Rubin - JGI Director UC MERCED Sam Traina - Vicechancellor of Research

  14. Make JGI a resource for curricula, tools, and raw material for genomics education EDUCATION DEPARTMENT Your School Here

  15. Learn how to design/implement undergraduate genomics research projects and courses Learn how to use IMG(M) as an instruction tool Learn to use sequence as the raw material for undergraduate research EDUCATION DEPARTMENT Bring undergraduate educators to the JGI to:

  16. Students annotate complete microbial genomes Requires only computer lab space Potential for collaboration across the curriculum Students work with real data, tools and databases Applying basic concepts in biochemistry, physiology, and evolutionary biology ADOPT-A-MICROBEGEBA Pilot year 2007-2008

  17. Contact Cheryl Kerfeld ckerfeld@lbl.gov EDUCATION DEPARTMENT Your School Here

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