See Also BISB 2018-19
See here for a list of projected course offerings for 2018-19.
All Core and Elective courses for the degree must be taken for a letter grade. Students must obtain a “B” or better in courses taken for the degree. If you receive a “B-” or lower in a Core or Elective class, or you take it on S/U grading, it does not fulfill your requirements. Please see the Grades FAQ if you have any grades of “B-” or lower or “U”.
Core Requirements for the Bioinformatics and Systems Biology Track
Each student in the Bioinformatics and Systems Biology Track must take four core courses. The three on this first list are required for all students:
- Bioinformatics II (BENG 202/CSE 282). Introduction to Bioinformatics Algorithms (4 units)
- Bioinformatics III (BENG 203/CSE 283). Genomics, Proteomics, and Network Biology (4 units)
- Bioinformatics IV (MATH 283). Statistical Methods in Bioinformatics (4 units)
For the fourth core class, choose one of the following. In the event that a student completes two or more of these with suitable grades, one will count as core and the other(s) as electives.
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 the ethics course BNFO 294 (previously 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 WebReg as well as via the "Scientific Ethics" 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 WebReg is necessary for students to receive course credit. To take it in the summer, register on ethics.ucsd.edu, and give the "certificate of completion" to the BISB graduate coordinator, in lieu of BNFO 294 credit on your transcript.
- BNFO 294. Scientific Ethics (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 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 (BENG 501, BGGN 500, CHEM 500, CSE 500, MATH 500, etc.), 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 Assistantship (2–4 units)
Each student in the Bioinformatics and Systems Biology track will select 16 units of Elective Courses from the Elective Fields (BIO, CS, SB, BMI, QBIO) delineated below, with at least 4 units from the CS series and 4 units from the BIO series. For example, a student interested in Systems Biology could take one 4 unit class from the CS series, one from the BIO series, one from SB-1, and one from SB-2.
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.
If a class is available both as an elective and as a core class, it may only be used to satisfy one of those requirements, not both.
Elective BIO-1: Biochemistry
- BENG 230A. Biochemistry (4 units)
- CHEM 209. Macromolecular Recognition (4 units)
- CHEM 213A. Structure of Biomolecules and Biomolecular Assemblies (4 units)
- CHEM 213B. Biophysical Chemistry of Macromolecules (4 units)
- CHEM 216. Chemical Biology (4 units)
Elective BIO-2: Molecular Genetics
- BICD 100. Genetics (4 units)
BGGN 220DEF are three consecutive 3.3 week classes, usually taken together, but that's not required.
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 I (4 units)
- MATH 281A. Mathematical Statistics (4 units)
- MATH 281B. Mathematical Statistics (4 units)
- MATH 284. Survival Analysis (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 264. Principles of Biomedical Informatics (4 units) – This core class for the BMI track may be taken as an elective for the BISB track.
- MED 265. Informatics in Clinical Environments (4 units)
- MED 267. Modeling Clinical Data and Knowledge for Computation (4 units)
- MED 268. Statistics Concepts for Biomedical Research (4 units)
- MED 269. Clinical Decision Support Systems at the Point of Care (4 units)
- MED 273. Communicating Biomedical Informatics (4 units)
- MED 276. Grant Proposal Writing Practicum (2 units)
- MED 277. Introduction to Biomedical Natural Language Processing (4 units)
Elective QBIO-1: Quantitative Biology
- BENG 226. Foundations of Biomechanics (4 units)
- BENG 235. Molecular Imaging and Quantitation in Living Cells (4 units)
- BGGN 214. Introduction to Q-Biology (4 units) – This may be applied to the BIO area elective requirement.
- MAE 263. Experimental Methods in Cell Mechanics (4 units)
- PHYS 273. Information Theory and Pattern Formation in Biological Systems (4 units)
- PHYS 274. Stochastic Processes in Population Genetics (4 units)
- PHYS 275. Fundamentals of Biological Physics (4 units)
- PHYS 277. Physics of the Cell (4 units)