Computational Genome Biology 2006-2007

Center for Genome Research & Biocomputing Oregon State University, 3021 ALS Bldg, Corvallis, Oregon 97331-7303 T 541-737-3347 | F 541-737-3045 | http://www.cgrb.orst.edu

PROGRESS REPORT – Year 3 COMPUTATIONAL AND GENOME BIOLOGY INITIATIVE August 2, 2007 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. B. Continue Renovation of MCB Curriculum. Substantial progress on continued MCB Graduate curriculum renovation, formation of new courses, and final instructional plans for the new faculty to teach in the MCB Graduate Program was made. 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: Summer MCB525 Molecular techniques (3)

Total credits

(3)

Fall MCB554 Genome structure, organization & maintenance (4) MCB511 Research perspectives (3) MCB610 Internship* (3) (10)

Winter MCB555 Genome expression (4) MCB668 Bioinformatics & programming (2+2) MCB610 Internship* (3) (11)

Spring MCB556 Cell & developmental biology (4) MCB557 Scientific skills & ethics (3) MCB610 Internship* (3) (10)

Changes from current core curriculum: i) Consolidation of 3-credit MCB553 (Structure and function of eukaryotic cells) and 3credit MCB556 (Cell signaling and development) into a single 4-credit course entitled Cell & developmental biology (MCB556), to be offered Spring Quarter. ii) Addition of MCB668 (Bioinformatics & Programming) to be offered as two 2-credit modules. iii) Require students to give an end-of-term seminar on their rotation project as part of their MCB610 Internship.

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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 reformulation 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. iii) MCB637 Host-Microbe Interactions (Team-taught, Dan Rockey, Organizer). This course was offered for the first time in Winter, 2007. The course explores principles of pathogenesis, symbiosis and interactions of hosts with microbes. c. Instructional Plans for CGBI Faculty in the MCB Graduate Program i) M. Freitag – Co-teach MCB555 (Genome Expression); Teach and organize MCB 511 (Research Perspectives) ii) E. Bakker – Co-teach MCB6XX (Genome Evolution); Co-teach MB/MCB668 (Bioinformatics and Programming) iii) T. Mockler - Co-teach MCB555 (Genome Expression); Co-teach MB/MCB668 (Bioinformatics and Programming) iv) J. Chang – Co-teach MCB554 (Genome Organization and Maintenance); Co-teach MCB637 (Host-Microbe Interactions) v) D. Denver – Co-teach MCB6XX (Genome Evolution); Co-teach MCB554 (Genome Organization and Maintenance) 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. D. Computational Infrastructure Expansion and Development of New Core Facilities. We made substantial upgrades and expansions to several components within the CGRB computational infrastructure, and developed a new core facility for high-throughput DNA sequencing within the CGRB. a. Computational Infrastructure. A significant build-out of the CGRB computational infrastructure occurred (http://genome.cgrb.oregonstate.edu/). This included addition of three new sub-clusters within Genome (the CGRB compute cluster), expansion of storage capacity to accommodate the new

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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. 2. Goals for 2007-08 A. New Graduate Students in MCB Program. We will continue attracting and elevating the profile of graduate students in computational and genome biology in the MCB Graduate Program. 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. C. Expansion of High-Throughput Sequencing Facility and Computational Infrastructure. We intend to upgrade several components within the CGRB computational infrastructure, including addition of new cluster nodes that are dedicated for use by new faculty programs. 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. 3. Where you want to be when your initiative is fully developed/matured? • Major strength in Computational and Genome Biology at OSU. Strong impact on existing departments and programs through infusion of new faculty, new graduate students and new or revised core facilities. We envision OSU being recognized as a major force in these areas of science, which will serve to attract students, faculty, postdoctorals and stature to OSU. • Recognition as an excellent destination for graduate students in computational and genomebased biology. They will be accommodated through formulation of a new track – Computational and Genome Biology – within the MCB Graduate Program. • Major new community resources and core facilities, primarily through the CGRB, enabling high-throughput and computation-intensive bioscience. This will serve to attract new grant money broadly across OSU. • Recognition as a center of high-impact discovery, attracting donors and gift-givers to OSU.

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4. A few simplified metrics that will be easy for others to understand • Leveraged approximately $3.1 million from CGRB, Research Office and Colleges to combine with Provost’s Initiative funds. • Funds originally proposed for THREE new faculty were leveraged to provide support for FIVE new faculty in four departments. • Within five years, each faculty is projected to generate $450,000/yr in external grant funding. • Both salary and start-up packages offered are recognized as peer-competitive by our external advisors (Brian Staskawicz of UC Berkeley, and Steve Kay of The Scripps Research Institute). • Five new or revised courses to be offered by MCB Graduate Program within two years. 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)

Progress Report prepared by: James C. Carrington Director, Center for Genome Research and Biocomputing, and Co-coordinator, Computational and Genome Biology Initiative