Transcript The Joint Genome Institute’s Microbial Genome Annotation Program for Undergraduates Opportunities for Students to Help Write the Genomic Encyclopedia of Bacteria and Archaea Cheryl A.

The Joint Genome Institute’s Microbial
Genome Annotation Program for
Undergraduates
Opportunities for Students to Help Write
the Genomic Encyclopedia of
Bacteria and Archaea
Cheryl A. Kerfeld
DOE Joint Genome Institute
Dept. of Plant and Microbial Biology, UC Berkeley
Training the Next Generation of Scientists
DOE Education
What is the JGI?
What is the JGI?
JGI
G5
DOE Mission & Sequence-based research
Broad (MIT) Biomed
Wash U
Biomed
Baylor
Biomed
Venter
Biomed
Current major initiative:
The Genomic Encyclopedia of Bacteria and Archaea
JGI: Training the Next Gen
The need to update the curriculum
• In contrast to biological
research, biology education
has changed relatively little in
the past two decades
• Involving students in research
is the best way to inspire
students to the goal of a
career in science
Replacing traditional lab experience…
Embed Research in Undergrad Labs and Courses
TNGS at the PGF
Gene Annotation
• Determining the biological role of all gene
products is the principal objective of genome
analysis.
• This involves searching for biochemical and
evolutionary relationships, incorporating
phenotype and ecotype information.
Extrapolation
Involving students in Annotation
• Requires only computer lab space
• Bioinformatics algorithms provide a new,
untapped way to illustrate the principles of
biology
• Students work with real data, tools and
databases—to become discerning users
• Applying basic concepts in biochemistry,
physiology, and evolutionary biology
• A Dedicated Student (or Broader Impact)
Research Project that Scales
Independent
Research
Introductory
Molecular
Biology
Molecular &
Cell Biology
Ecology and
Evolutionary
Biology
Introductory
Bioinformatics
Biochemistry
Microbiology
General
Education
The JGI Provides
• Genome sequence in an integrated research
database (IMG)
• Annotation toolkits for students and faculty
• (IMG-ACT)
• Faculty training & networking
• DATA (GEBA)
The JGI Provides
• Genome sequence in an integrated research
database (IMG)
• Annotation toolkits for students and faculty
• (IMG-ACT)
• Faculty training & networking
• DATA (GEBA)
The JGI Provides
• Annotation toolkits for students and faculty
(IMG-ACT)
IMG ACT
• Annotation Management Tools for Instructors
• Web-based lab notebook with links and tutorials for
students (wiki)
IMG ACT
• Annotation Management Tools for Instructors
• Web-based lab notebook with links and tutorials for
students (wiki)
• Course management tools
– Assigning genes and pathways
– Reviewing student annotations
• Instructor support forum (wiki)
• “Report” format for export of annotations—confidence
levels
IMG ACT
• Annotation Management Tools for Instructors
• Web-based lab notebook with links and tutorials for
students (wiki)
• Course management tools
– Assigning genes and pathways to individuals and teams
– Reviewing student annotations
• Instructor support forum (wiki)
• “Report” format for export of annotations—confidence
levels
• Student Lab Notebook (Wiki)
• Student Annotation Report (data port to IMG)
Modular Annotation
Student Tools: Wiki Format Notebook
Publishing Annotations
– Functional Genomics
– Publication
– Port back into IMG
• QC
• “Genebook”—combine social
Networking and annotation
Instructor Tools
The JGI Provides
• Genome sequence in an integrated research
database (IMG)
• Annotation toolkits for students and faculty
• (IMG-ACT)
• Faculty training & networking
• DATA (GEBA)
Faculty Development:
Using Bioinformatics to Illustrate
• The logic of the algorithm
• In silico translation
• Alignments and evolution (selection of
scoring matrices)
• Conservation at the level of protein structure
• Gaps as insertion/deletion events
• Evolution by combination of domains (the
power of local alignments)
2008-2009 Pilot Faculty Team
I want to be
able to do Y
I want tool X
The JGI Provides
• Genome sequence in an integrated research
database (IMG)
• Annotation toolkits for students and faculty
• (IMG-ACT)
• Faculty training & networking
• DATA (GEBA)
The Genomic Encyclopedia of
Bacteria and Archaea
Expansions
• IMG-ACTM --in progress
• Expand current annotation program to High School
• Functional Genomics- with academic partners
• Bioinformatics Education Clearinghouse
(with PLoS Biology)
How to Get Involved
http://www.jgi.doe.gov/education/
How to Get Involved
http://www.facultyprograms.org/page02a.shtml
Summary
• The JGI Genome Annotation Program
involves students in interpreting genome
sequence data—for use across the
curriculum
• We provide faculty training and bioinformatic
tools that can be used to involve large
numbers of students in research
• The Next Phases:
– Extend to high school students
– IMG-ACTM
– Build functional genomics program to test annotation
hypotheses
– Euks
Acknowledgements
• Pilot Faculty—Brad Goodner, Hiram College and
Kathleen Scott, U. South Florida
• JGI Informatics: Rene Perrier, Joni Fazo,
• David Hays, Anthony Kosky, Yakov Golder
• IMG Team (Victor Markowitz, Nikos Kyrpides et al.)
• Jonathan Eisen and GEBA Group
• Edwin Kim, Seth Axen