UCSF

Curriculum

All curriculum is subject to change due to the COVID-19 pandemic.

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Requirements

Year one requirements

Term Required courses Other requirements
Late summer

Bootcamp

  • Math/Matlab
  • Biology Didactic
  • Molecular Biology
  • Biochemistry
 

Fall term

  • BP 204A Macromolecular Interactions

Required:

  • Two fundamental modules, selected from: Physical Chemistry, Programming
  • Online Stats Course with TA Sessions (can take in year 1 or 2)
  • Race & Racism in Science

Complete First Rotation

Journal Clubs (QBC and BP)

Pizza Talks

BBC Seminars

 

Winter term

Complete Proposal and Mini Oral

Required:

  • BP 204B Macromolecular Methods

And select one of the below:

  • BP 205B Dynamical Systems Modeling (required for the CBS emphasis)
  • BMI 203 Algorithms
  • Chem 241 Molecular Thermodynamics
  • Bioreg (Tetrad course)
  • Systems Pharmacology (PSPG 245B)
  • Non Biophysics course approved by academic advisor

Complete Second Rotation

Journal Clubs

Seminars

Pizza Talks

Spring term

Students will take the Ethical Conduct of Science course in Spring of year 1.

3 mini courses

Complete third Rotation

Journal Clubs

Seminars

Pizza Talks

End of spring

Optional: Systems Biology Emphasis (Must be declared at time of qualifying exam. Must take BP 205B.)

 

Year one notes

  1. Bootcamp: Two-week immersion that provides basic competency and breadth before the start of the formal curriculum. Fosters group cohesion while breaking down barriers of scientific communication and provides a level playing field.
  2. Rotations: 3 ten-week rotations starting Fall quarter. Must include at least 1 experimental and 1 computational. The ability to have an on-campus rotation this year will be made by a case by case basis. Details: Rotations and Advisor Selection.
  3. Curriculum selection: While program selection is not required until end of spring, appropriate corresponding coursework must be taken. If corresponding coursework is not taken in year one, it must be completed in year two.
  4. Mini courses: Two-week elective courses in Spring that allow for diversification of curriculum. Each student will take 3 mini courses in spring quarter. One of them must be outside Biophysics.
  5. Fundamentals: Two to three-week elective courses in Fall that allow for diversification of curriculum.
  6. Advising: Rotations and coursework must be approved by your assigned academic advisor.

Additional year one requirements

Course Course information Description

Lab rotations

BP 215

Fall/Winter/Spring

3 units each, 3 rotations

3 ten - week rotations (one per quarter), at least 1 experimental, 1 computational

Details: Rotations and Advisor Selection.

Biophysics Journal Club

BP 223

Fall/winter/spring

1 unit
This seminar provides graduate students with a forum in which to develop seminar and poster presentation skills, critically organize and critically review scientific data, and analyze and question oral scientific presentations.

QBC Journal Club

BMI 223

Fall/winter/spring

1 unit

Journal club presentations by first- and second-year students in iPQB, CCB, and PSPG graduate programs.

Details: QBC Journal Club Requirements.

Graduate research opportunities

BMI 224

Fall/winter

1 unit

Faculty-student talks

Additional requirements for the duration of your time in the program

Course Course information Description

Research Seminars

BP 220

Fall/winter/spring

1 unit

Research seminars presented by visiting scientists

QBC Retreat NA All students are required to attend the annual QBC Retreat.

Year two requirements

Course Course information Description

Oral qualifying examination

Must complete by end of second year

(If selecting an emphasis in Complex Biological Systems, this must be declared at time of qualifying exam)

Research

(every quarter, year two and forward)

BP 250

Fall/winter/spring

1-8 units

Research in your thesis lab; sign up every quarter in years two to six

Teaching Assistantship

Fall/winter/or spring

One quarter teaching assistant position

Biophysics Journal Club

(every quarter offered, year two and forward)

BP 223

Fall/winter/spring

1 unit

This seminar provides graduate students with a forum in which to develop seminar and poster presentation skills, critically organize and critically review scientific data, and analyze and question oral scientific presentations.

QBC Journal Club

BMI 223

Fall/winter/spring

1 unit

Journal club presentations by first- and second-year students in the iPQB, CCB, and PSPG programs

Details: QBC Journal Club Requirements

Grant Writing

BP 297

Fall

1 unit

Support for fellowship applications
QBC Retreat NA All students are required to attend the annual QBC Retreat

Year three requirements and beyond

Course Course information Description

Advancement to candidacy

Within 6 months following qualifying examination

 

Annual thesis meetings, year three and forward

On or around the anniversary of your qualifying examination

Thesis meetings are to be held at least once per year following completion of oral examination

Those who have not graduated by Winter of 6th year must retake Ethical Conduct of Science

Neuroscience 214

Spring 1 unit

Ethical Conduct of Science must be taken once every 4 years
QBC Retreat NA All students are required to attend the annual QBC Retreat
DEI Leadership Course NA All advanced students are required to take this course

Details: Advancement to candidacy and thesis progression.

Sometime in either the fourth or fifth year all students give a talk on their research at the iPQB program retreat.

Students are expected to graduate within six years of starting the program. Details: Six-year policy. In order to graduate you must submit your thesis to the Graduate Division and give a thesis seminar. Extending time in the program beyond six years is subject to the approval of the iPQB Executive Committee.

Courses and course materials

Listed below are course requirements and suggestions to optional helpful coursework for the Biophysics Graduate Program, including course name and number, quarters offered, units, and instructors.

Required core courses

BP 204 A and B: Macromolecular Structure and Interactions

Fall/Winter
4 units each
James Fraser,  John Gross, Aashish Manglik in Fall, Robert Stroud and Oren Rosenberg in Winter

BP 204A: In this course, we will pursue a qualitative and quantitative understanding of the physical basis of macromolecular function. We will examine: the nature and quantification of the forces that drive macromolecular interactions, both intramolecular (macromolecular folding), and with other proteins and ligands; diffusion of macromolecules; the structural underpinnings of the kinetics and thermodynamics of macromolecular reactions; and the physical basis of important biophysical methods. We will examine the distinctions for macromolecules residing in lipid bilayers. The classwork will be mostly interactive with a weekly lecture that informs in class problem solving and discussion of relevant classic and current literature.

BP 204B: Fluency in multiple biophysical methods is often critical for answering mechanistic questions. To train the next generation of biophysicists at UCSF, we have decided to alter the traditional didactic structure by creating a new 6 week “Macromolecular Methods” class that places data collection at the beginning of the course.

BP 205 B: Dynamical Systems

Winter
4 units
Hani Goodarzi

Dynamical Systems Modeling (Required only for those with a designated emphasis in Complex Biological Systems, elective for others)

Our re-imagined 2017 systems biology class will tackle the challenge of identifying governing principles of an immensely complex and interconnected cellular signaling hub. The class will self-organize into teams that develop strategies to identify, analyze and model interconnections and consequences of this hub organization. Diverse data sets will include—but not be limited to—high-content image based screens, protein-protein interaction and drug response profiles of perturbations to the hub and its partners. The 10-week class will be organized by:

1: Literature review and proposals

2-6: Data acquisition and analysis

7-8: Integration and validation of results

9-10: Draft of manuscript and presentations.

Our systems biology class will have an unprecedented opportunity to make exciting scientific discoveries based on unpublished data.

BMI 206: Statistical Methods for Bioinformatics

Fall
3 units
Katie Pollard

Broad survey of bioinformatics with accompanying assignments. Topics covered include genomics, database searching, family/super-family analysis, structural genomics, complex systems, genetic circuits, and protein-protein interactions.

BMI 203: Biocomputing Algorithms

Winter
3 units
Andrej Sali

Introduction to computational issues and methods used in the fields of bioinformatics and computational biology. This course emphasizes the implementation, analysis, and validation of methods. It is about attacking computational problems in biology and not the expert use of existing tools. Areas addressed include analytical thinking, problem decomposition, and algorithm design and implementation. Assignments will focus on the design and implementation of key bioinformatics algorithms.

CHEM 241: Molecular Thermodynamics

Fall
5 units
Michael Grabe

This is a course on molecular thermodynamics and statistical mechanics in a biological context. It covers the concepts of entropy, enthalpy, free energy, ligand binding, solvation; the properties of water and the hydrophobic effect; solution electrostatics; adsorption; physical and chemical kinetics; polymer properties; and single-molecule dynamics. Each week of the course consists of two lectures focusing on fundamental principles, and one paper discussion session aiming at connecting these physical principles to problems in biology such as enzyme catalysis, protein folding and phase-transitions, and chromatin compaction.

BP 219: Special Topics in Biophysics (fundamentals and mini courses)

Fall
3 units
Staff

Biophysics faculty combine to offer courses on important areas of Biophysics in preparation for beginning of the cohort's graduate school career.

Spring
3 units
Staff

UCSF Basic Science Graduate Programs collaborate to offer elective courses that allow for diversification of curriculum.

Minicourses

Other requirements

BP 215: Laboratory Rotations (3 rotations over 3 quarters)

Winter/Spring (first year only)
2 units each rotation

BP 220: BBC Seminar Series

Fall/Winter/Spring
1 unit each
Selected topics by guest lecturers

BMI 223: Critical Topics in Biomedical Informatics (QBC Journal Club)

Fall/Winter/Spring
1 unit each
Brian Shoichet

QBC Journal Club, critical review of published scientific papers from scholarly journals, including comprehension, analysis, and evaluation of published scientific data.

QBC Journal Club Requirements

BP 223: Scientific Communication Seminar (BP Journal Club)

Fall/Winter/Spring
1 unit each
Tanja Kortemme

BP Journal Club, forum in which to develop seminar and poster presentation skills, critically organize and critically review scientific data, and analyze and question oral scientific presentations.

BMI 224: Graduate Research Opportunities Seminar (BBC Pizza Talks)

Fall/Winter
1 unit
Ryan Hernandez

This course offers first-year students a series of weekly presentations on research interests of basic science faculty. The purpose is to acquaint new graduate students with research projects and opportunities in faculty laboratories.

BP 297: Special Study (NSF Workshop)

Fall
1 unit
Zev Gartner

First-year students meet weekly to hone their grant-writing skills with the objective of submitting a fellowship proposal to the National Science Foundation.

GRAD 214: Ethics and the Responsible Conduct of Research

Spring first year, eight sessions
1 unit
Faculty

Sessions cover data management, animals in research, human subjects in research, rules and etiquette of publications, procedures and rules of grants, corporate-academic interactions.

Optional online coursework

The following are suggestions from our students to other resources that can be helpful in this program:

  • For statistics: OpenIntro - free online course, free textbook
  • Class Central - a list of free online courses
  • Udacity - very engaging, about 3 to 5 hours per course