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1. What was accomplished in 2006-2007? Several goals were articulated in the previous report.
A. New Graduate Students in MCB Program. We continued attracting and elevating the profile of
graduate students in computational and genome biology in the MCB Graduate Program. Eight new
Ph.D. students entered the MCB Graduate Program. Two new students, William Thomas and Sam Fox,
were provided CGBI-funded GRA positions in recognition of their qualifications and interests in
computational and genome-based biological research.
a. MCB Curriculum Renovation. During the MCB Faculty Workshop (see below), consensus for
how to revise the MCB Ph.D curriculum was reached. This will compress the cell biological
component, and provide room for a new course in Bioinformatics. The proposed new core
curriculum is as follows:
b. Formation of New MCB Courses. Needs for additional training in computational biology,
principles of genome evolution, and host-microbe interactions are being met by addition of three
new courses:
i) MB/MCB668 Bioinformatics and Programming (2+2 Cr). This is actually a re-
formulation of an existing 4-Cr lab course (The Molecular Evolution of Cells and
Organelles). The first 2-Cr module will cover Basic Bioinformatics (Instructors – Erica
Bakker and Steve Giovannoni). The second 2-Cr module will cover hands-on
programming for the biologist (Instructors – Todd Mockler and Scott Givan).
ii) MCB6XX Genome Evolution (Instructors – Dee Denver and Erica Bakker). This
course will apply mathematical, genomic and evolutionary principles to teach students how
genomes evolve.
iv) J. Chang – Co-teach MCB554 (Genome Organization and Maintenance); Co-teach MCB637
(Host-Microbe Interactions)
C: MCB Faculty Workshop. This occurred December 12-13, 2007, at the Salishan Resort in
Gleneden Beach, OR. The primary objective of the workshop was to finalize plans for revision and
renovation of the MCB program, with particular emphasis on the instructional component. The
workshop was attended by 27 faculty and 2 current Ph.D students. A report was prepared and submitted
to the Provost as part of the MCB Program review.
Illumina system, and addition of new servers. The CGBI faculty were instrumental in funding part
of this expansion, and in developing novel software and applications using these facilities
(http://cgbi.cgrb.oregonstate.edu/resources).
b. Development of High-Throughput Sequencing Facility. The CGBI developed a new facility for
cutting-edge genomics in the CGRB Core Labs. The facility involved purchase of an Illumina 1G
DNA sequencing system (http://corelabs.cgrb.oregonstate.edu/hts), which provides a revolutionary
increase in capacity and applications over existing DNA analysis systems. The Illumina system was
purchased through a major pooling of start-up funds from CGBI faculty, from existing grant funds,
and from a RERF grant.
E. New Grant Funding. Grants to the CGBI faculty included: An equipment grant ($130,000) to
partially fund the Illumina 1G system; NIH, NSF and DOE grants to individual faculty. Several
graduate training grant proposals (including NSF IGERT, USDA National Needs) were submitted and
pending.
B. Continue Renovation of MCB Curriculum/New Courses. The major goals for the upcoming
year include completion of upgrades to four existing courses, and initiation of two new courses in
genome evolution and bioinformatics. We also plan to implement a new track – Genome Biology – for
specialized training within the MCB Graduate Program.
D. New Grant Funding. Besides grants to individual CGBI faculty, we seek to obtain additional
group grants for training graduate students and for development of shared use research facilities.
5. Other helpful information (examples include student credit hours that will be/could be
generated; new dollars that will be generated from the dollars invested; a summary of what OSU
gets for this investment)
• In addition to research funding to new faculty, the Initiative and new CGRB investment will
continue to fuel high-value, grant-generating activities from existing programs. Examples of early
payoffs from these investments include funding for projects like the Ocean Microbial Genome project
($3.3 million, Moore Foundation; PI: Giovannoni, CGBI co-coordinator), Arabidopsis Small RNA
project (Total $2.9 million over 6 years, NSF; PI: Carrington, CGBI co-coordinator), and new grants
for CGBI faculty (see above)
James C. Carrington
Director, Center for Genome Research and Biocomputing, and
Co-coordinator, Computational and Genome Biology Initiative