Advancing Science with DNA Sequence 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

Advancing Science with DNA Sequence 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

Advancing Science with DNA Sequence 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

Advancing Science with DNA Sequence

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

Advancing Science with DNA Sequence 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

Advancing Science with DNA Sequence 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

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

Advancing Science with DNA Sequence INSTRUCTORS 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

Advancing Science with DNA Sequence MINI-JAMBOREE Organized by JGI Informatics Department (Annotation Group, Igor Grigoriev) Genome annotation workshop at JGI + JGI Tour

Advancing Science with DNA Sequence 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

Advancing Science with DNA Sequence ASSESSMENT 3 mid-term examinations students presented their projects in the last sessions of the course written reports

Advancing Science with DNA Sequence FEEDBACK individual speaker evaluation forms final course evaluation forms + initial survey for next year

Advancing Science with DNA Sequence 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

Advancing Science with DNA Sequence EDUCATION DEPARTMENT Make JGI a resource for curricula, tools, and raw material for genomics education Your School Here

Advancing Science with DNA Sequence EDUCATION DEPARTMENT 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 Bring undergraduate educators to the JGI to:

Advancing Science with DNA Sequence ADOPT-A-MICROBE GEBA Pilot year 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

Advancing Science with DNA Sequence EDUCATION DEPARTMENT Contact Cheryl Kerfeld Your School Here