advancing science with dna sequence undergraduate genomics in a research university environment a...

Advancing Science with DNA Sequence

Undergraduate Genomics in a Research University

EnvironmentA Collaborative Effort between the JGI and UC Merced

M. Pilar FrancinoDOE Joint Genome Institute

Miriam Barlow and Mónica MedinaUniversity of California, Merced


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


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


11 undergraduate students (mostly upper division) &

3 graduate students

Spring semester 2007


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 andmethodologies in genome science


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


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


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


MINI-JAMBOREE

Organized by JGI Informatics Department (Annotation Group, Igor Grigoriev)

Genome annotation workshop at JGI +JGI Tour


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


ASSESSMENT

3 mid-term examinations

students presented their projects in the last sessions of the course

written reports


FEEDBACK

individual speaker evaluation forms

final course evaluation forms

+

initial survey for next year


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


EDUCATION DEPARTMENT

• Make JGI a resource for curricula, tools, and raw material for genomics education

Your School Here



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:


ADOPT-A-MICROBEGEBA Pilot year 2007-2008

• 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



• Contact Cheryl Kerfeld [email protected]

Your School Here

advancing science with dna sequence undergraduate genomics in a research university environment a...

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