See Also BMI 2013-14
See here for a list of projected course offerings for 2013-14.
Core Requirements for the Biomedical Informatics Track
Each student in the Biomedical Informatics Track must take the four courses below.
- Bioinformatics II (BENG 202/CSE 282). Introduction to Bioinformatics Algorithms (4 units)
- MED 264. Principles of Biomedical Informatics (4 units)
- Bioinformatics IV (MATH 283). Statistical Methods in Bioinformatics (4 units)
- BNFO 285. Statistical Learning in Bioinformatics (4 units)
All students in years 1-2 must take the Colloquium for their track in fall, winter, and spring quarters.
All students in years 1-2 must take the Student Research Talks in fall, winter, and spring quarters.
All students must take one of the two ethics courses, SOMI 226 or BIOM 219, by the end of the second year. However, funding sources may require that it be taken the first year, so we recommend taking it the first year.
Special registration procedure: Students must register for the ethics course both via TritonLink as well as via the registration form on ethics.ucsd.edu. The course is taken by many UCSD employees (not just students), so the Ethics Program uses its own registration form. Registration on TritonLink is necessary for students to receive course credit.
- SOMI 226. Scientific Ethics (1 unit)
- BIOM 219. Ethics in Scientific Research (1 unit)
Research and Teaching Requirements
During the academic year, all students must be enrolled in the appropriate research course for their level. Students typically do three rotations in year 1 (BNFO 298) and then do research units (BNFO 299) with their thesis advisor in years 2 and later. BNFO 299 units may be varied to meet the full-time enrollment requirement of 12 units per quarter in fall, winter, and spring. During the summer, students are expected to do research as well, but should not enroll in BNFO 298 or BNFO 299. During all quarters and the summer, students are responsible for satisfying program requirements including proposals, reports, presentations, committee meetings, notifying the graduate coordinator when joining/changing labs, etc.; the only difference is that students do not enroll in BNFO 298 or BNFO 299 in the summer. In addition, each student will make periodic research presentations to the graduate program students/faculty. Students will also discuss their progress at the annual program meeting to be held each year.
- BNFO 298. Research Rotation (4–8 units)
- BNFO 299. Graduate Research (1–12 units)
All students must serve as a teaching assistant (TA) for at least two quarters. Students should enroll in BNFO 500 (Teaching Experience) or an equivalent course code in another department, during each quarter in which they are a teaching assistant. A typical teaching assistantship is 110 hours/quarter (25% load, 2 units of BNFO 500); however, this varies by class. 220 hours/quarter is a 50% load, 4 units.
- BNFO 500. Teaching Experience (2–4 units)
Each student in the Biomedical Informatics track will select 16 units of Elective Courses from four distinct Elective Fields (BIO, CS, SB, BMI) delineated below, with at least 4 units from the CS series and 8 units from the BMI series.
It is the general policy of the program to be as adaptable as possible to the needs of the individual student. The curriculum committee is receptive to students petitioning to satisfy an Elective requirement by taking a course not listed among the Electives.
Elective BIO-1: Biochemistry
- BENG 230A. Biochemistry (4 units)
- CHEM 209. Macromolecular Recognition (4 units)
- CHEM 213. Physical Chemistry of Biological Macromolecules (4 units)
- CHEM 216. Chemical Biology (4 units)
Elective BIO-2: Molecular Genetics
- BICD 100. Genetics (4 units)
- BGGN 220. Graduate Molecular Biology (6 units)
- BGGN 223. Graduate Genetics (6 units)
Elective BIO-3: Cell Biology
- BICD 110. Cell Biology (4 units)
- BICD 130. Embryos, Genes, and Development (4 units)
- BGGN 222. Graduate Cell Biology (6 units)
- CHEM 221 / BGGN 230. Signal Transduction (4 units)
Elective CS-1: Algorithms
- CSE 101. Design and Analysis of Algorithms (4 units)
- CSE 200. Computability and Complexity (4 units)
- CSE 202. Algorithm Design and Analysis (4 units)
- CSE 280A. Algorithms in Computational Biology (4 units)
- MATH 261A. Probabilistic Combinatorics and Algorithms (4 units)
Elective CS-2: Machine Learning and Data Mining
Elective CS-3: Mathematics and Statistics
- MATH 274. Numerical Methods for Physical Modeling (4 units)
- MATH 280A. Probability Theory (4 units)
- MATH 281A. Mathematical Statistics (4 units)
- MATH 281B. Mathematical Statistics (4 units)
- PHYS 210A. Equilibrium Statistical Mechanics (5 units)
- PHYS 210B. Nonequilibrium Statistical Mechanics (4 units)
Elective SB-1: Biological Systems
Elective SB-2: Kinetic Modeling
Elective BMI-1: Biomedical Informatics
- MED 263. Bioinformatics Applications to Human Disease (4 units)
- MED 265. Introduction to Clinical Environments (2 units)
- MED 266. Machine Learning in Biomedicine (4 units)
- MED 267. Modeling Clinical Data and Knowledge for Computation (2 units)
- MED 269. Clinical Decision Support Systems at the Point of Care (4 units)
- MED 276. Grant Proposal Writing Practicum (2 units)