Course Requirements | Bioinformatics and Systems Biology

See here for a list of projected course offerings for 2024-25. For departments/classes that have not announced projected schedules, contact the instructor(s) or department for information.

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

Core classes must be completed in the first two years, and usually are completed the first year.

Each student in the Bioinformatics and Systems Biology (BISB) track must take four core courses:

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)
One class selected from the “Fourth Core Class” options below (except BENG 203/CSE 283).

Each student in the Biomedical Informatics (BMI) track must take four core courses:

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)
One class selected from the “Fourth Core Class” options below.

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. (If an additional fourth core class is not on the list of electives, it can count towards the required 16 units of electives, but not towards an elective field requirement like CS or BIO.) Some options may not be offered every year; choose from options available by your deadlines.

CSE 280A. Algorithms in Computational Biology (4 units)
CSE 284. Personal Genomics for Bioinformaticians (4 units)
ECE 208. Computational Evolutionary Biology (4 units)
BNFO 286. 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: BNFO 281 for the BISB track, or MED 262 for the BMI track.

BNFO 281. Seminar in Bioinformatics and Systems Biology (1 unit)
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)

Ethics

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; in particular, all students on NIH training grants or other NIH funding are required to take ethics in their 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; please do both of these steps promptly when the courses open up, as they may fill quickly. 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)

Students must also take the Scientific Ethics Refresher Course every four years thereafter; e.g., students who take BNFO 294 in their first year should take the Refresher in years 5 and 9 (if still here). The Refresher course does not have a course number and will not appear on your transcript. Register for it on ethics.ucsd.edu only (not WebReg). Afterwards, give the “certificate of completion” to both the BISB Graduate Coordinator and your advisor (it may be needed for their grant report).

Research 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)

Teaching Requirements

All students must serve as a teaching assistant (TA) for at least two quarters. Please contact the BISB graduate coordinator by email in advance of each teaching assistantship to complete required paperwork and other administrative arrangements.

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. For summer teaching assistantships, please contact the BISB graduate coordinator to record it in lieu of BNFO 500 credit.

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.

Students are strongly encouraged to do only 25% teaching assistantships, due to the impact on time available for coursework and research. If you are considering a 50% position, please check if it can be split into two 25% positions. Please submit a petition to the BISB Curriculum Committee for any position with a load above 25%.

BNFO 500. Teaching Assistantship (2–4 units)

Program Electives

Each student must select 16 units of Elective Courses from the Elective Fields (BIO, CS, SB, BMI, QBIO) delineated below, according to the rules for their track. 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. Some options may not be offered every year; choose from options available by your deadlines.

Electives are started in the first year and usually completed within the first two years. However, the Second Year Qualifying Examination may be taken even if electives are not completed.

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 (see the Curriculum Petitions FAQ).

BISB track: Each student must take 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.

BMI track: Each student must take 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. (Students with a clinical background should replace MED 265 by MED 263.) 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.