Course Requirements (2018-19) | Bioinformatics and Systems Biology

See Also BMI 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 Biomedical Informatics Track

Each student in the Biomedical Informatics 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)
MED 264. Principles of Biomedical Informatics (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.

CSE 280A. Algorithms in Computational Biology (4 units)
ECE 208. Computational Evolutionary Biology (4 units)
BNFO 286/MED 283. Network Biology and Biomedicine (4 units)
Bioinformatics III (BENG 203/CSE 283). Genomics, Proteomics, and Network Biology (4 units) – This is core in the BISB track. In the BMI track, it may be taken as the 4th core class or as an elective.

Seminars

All students in years 1-2 must take the Colloquium for their track in fall, winter, and spring quarters.

MED 262. Current Trends in Biomedical Informatics (1 unit)

All students in years 1-2 must take the Student Research Talks in fall, winter, and spring quarters.

BNFO 283. Bioinformatics Student Research Talks (1 unit)

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)

Program Electives

Each student in the Biomedical Informatics 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 8 units from the BMI series. BMI students should take MED 265 and 267 as electives to fulfill DBMI's trainee requirements.

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.

DBMI trainees should see the DBMI website for information about additional requirements and other DBMI courses. Please consult your advisor about which courses are required depending on status related to funding, graduate program, etc.