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 |Fall |Winter |Spring | | |MCB525 |MCB554 |MCB555 |MCB556 | | |Molecular techniques |Genome structure, organization|Genome expression (4) |Cell & developmental | | |(3) |& maintenance (4) | |biology (4) | | | |MCB511 |MCB668 |MCB557 | | | |Research perspectives (3) |Bioinformatics & programming |Scientific skills & ethics | | | | |(2+2) |(3) | | | |MCB610 Internship* (3) |MCB610 Internship* (3) |MCB610 Internship* (3) | |Total |(3) |(10) |(11) |(10) | |credits | | | | |
Changes from current core curriculum:
i) Consolidation of 3-credit MCB553 (Structure and function of eukaryotic cells) and 3-credit 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.
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.
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...