Degree Progress Outline

Outline of degree progress can also be found in the program handbook (Stanford access required, version update 2023-24).


First Year

Courses & Research

Rotations (two up to three rotations)

  1. You will need to work on your first rotation prior to arriving / starting Autumn quarter on campus. Please make sure to contact your faculty of interest in summer, and update Kathleen/Amy on your Autumn quarter rotation.
  2. Kathleen/Amy will email you to check in on your rotation updates each quarter.

    Please note
    : You are expected to do rotations in Autumn, Winter, and/or Spring quarters. If a fourth rotation in Summer is necessary, or you are expecting to extend your rotation into Summer, you must obtain permission from the director ahead of time, and let Kathleen/Amy know.
Thesis Lab
  1. E-mail Kathleen/Amy when you decide on your research lab. If your advisor is not a Biophysics faculty, you will need to have a faculty who is in Biophysics as your co-advisor on your reading committee.

Individual Development Plan (IDP) - Biosciences requirement

  1. Complete your first IDP meeting with your advisor within 30 days of joining your thesis lab.
  2. IDP meetings are required annually, apart from Thesis Committee Meetings (see below).
  3. Update your record in Graduate Student Tracking (GST).

Course Requirements




BIOE 300A 

Biological Macromolecules

Molecular and Cellular Bioengineering




Methods in Molecular Biophysics
(offered every other year)



Seminar in Biophysics


MED 255

The Responsible Conduct of Research



AND, 4 graduate level courses in physical or biological science, with

at least 1 course in physical science
at least 1 course in literature-based biological science

Notes on Courses:

  1. Students should always register for 10 units total each quarter.
  2. All required courses must be taken with letter grade, except BIOPHYS 250 (C/NC) & MED 255 (P/N). A "C" grade will not be an acceptable grade.

Due to COVID-19, the Program counts all courses taken in academic year 2021-22 with a grade of 'CR' (credit) or 'S' (satisfactory) towards satisfaction of graduate degree requirements that otherwise require a letter grade provided that the instructor affirms that the work was done at a 'B-' or better level.

  1. The "+/-" grading basis is for MD students only.
  2. Prof. KC Huang, Director of the Biophysics Program, is your program advisor during your 1st year until you settle in a lab. Please register under KC for your research units (BIOPHYS 300). After you chose your research lab, you should register under your advisor’s name.


Second Year

Courses & Research

Prepare for your Qualifying Exam

Reading Committee

Form your Reading Committee and prepare for your Qualifying Exam. E-mail Kathleen/Amy when your Qual Exam date has been set, so we can send you the Qual Exam form (program form) and update your record.


You need to complete most or all of the course requirements by the end of second year, in order to be accepted into Candidacy. Candidacy applications should be filed by the beginning of your third year in the Program. After turning in your candidacy form, your candidacy status is valid for five years.

Individual Development Plan (IDP) - Biosciences requirement


Third Year

Courses & Research

Complete Qualifying Exam

  1. You are required to complete your Qualifying Exam by the end of Autumn quarter of your third year.
  2. After your Qualifying Exam, turn in your Qualifying Exam, Reading Committee, and Candidacy forms (3 forms total) to Kathleen/Amy.
  3. You will need to update your Qualifying Exam in GST, if you have trouble updating, please let Kathleen/Amy know right away.

Submit Qualifying Exam Form

  1. Regulations for the Qualifying Exam can be found here.
  2. Right after you've taken your exam, submit your Qualifying Exam Form to Kathleen/Amy.

Submit Reading Committee Form

  1. The form must be signed by all committee members and the director.
  2. Use HelloSign (free account sign-up) to obtain director and/or other committee members' signatures.
  3. Submit your Reading Committee Form to Kathleen/Amy.

Submit Candidacy Form

  1. The form must contain you, your advisor and the director's signatures (skip the middle column "Program Advisor"), with list of all required courses completed (see above "Course Requirements").
  2. You are not required to list all taken courses, only required courses listed will suffice, and must be listed.
  3. Use HelloSign to obtain director and/or other committee members' signatures.
  4. Submit your Candidacy Form to Kathleen/Amy.

Thesis Committee Meetings (TCM)* - Biosciences requirement  

  1. Your Qualifying Exam is considered your first Thesis Committee Meeting.
  2. Update your record in GST.

* Students are required to meet with advisory committee once a year in 3rd & 4th years, and twice for 5th years and above.

Individual Development Plan (IDP) - Biosciences requirement


Fourth Year

Courses & Research

Terminal Graduate Registration (TGR)

  1. Submit your TGR eForm in Axess when you reach 135 units. You must file your TGR form by the first day of the quarter you are to apply for. Kathleen/Amy will reach out to remind you ahead of time.
  2. Once your TGR status is approved, register under BIOPHYS 802 for your TGR units (not BIOPHYS 801).
  3. Graduates on TGR status can enroll in 0 - 3 units per quarter.

Thesis Committee Meetings (TCM) - Biosciences requirement

Individual Development Plan (IDP) - Biosciences requirement


Fifth Year & Above

Courses & Research

University Oral Examination (also Defense)

  1. Meet with Kathleen to discuss about your defense committee. Please fill, print, and bring your University Oral Examination Form with you to the meeting, available on the website.
  2. Complete your University Oral Examination with your defense committee.
  3. Please follow the University guideline, and submit your thesis to the University online.

Thesis Committee Meetings (TCM) - Biosciences requirement

Individual Development Plan (IDP) - Biosciences requirement


Additional Information

  1. Starting 2023-24, TA is required for Biophysics students, paid or without pay. This is not an annual requirement, and only needs to be done at least once during your graduate studies. Students will need to make TA arrangements with the course instructors, and let Kathleen / Amy know. For students who wish to opt-out, please send KC a request for approval, and cc Kathleen / Amy. This requirement does not apply for Structural Biology students.