Path to PhD Guidelines

From quals to graduation: guidance on student progression

Our goal is for all students to successfully complete their PhD. Formal policies are documented elsewhere; this document expands on those policies with ‘best practice’ guidelines for students and faculty. This document is provided by the Biophysics Executive Committee, which has broad responsibility for overseeing student progression, including both monitoring the progression of individual students, and making recommendations concerning policies and important issues such as time-to-degree.

Academic Advising

First years

Academic advisors are available to assist first year students in exploring rotation and curriculum options. First years are required to meet with the pre-assigned academic advisor prior to the start of classes and again prior to Winter and Spring.

Second years

Advisors are available to assist second year students in their preparation for the oral exam including brainstorming ideas for committee members. Second years are required to meet with the pre-assigned advisor once in the year.

Third years and up

Advising at any time is encouraged but is optional. Your advisor can help with the selection of thesis committee members, and can assist with any issues that come up throughout your time in the program. You may wish to make use of your advisor for advice related to any concerns you are having in your lab.

  • Qualifying Exam

    General timeline

    • 2-6 months before the oral examination, students must:
      • Consult with the research advisor and potential committee members.
      • Select fields for examination.
      • Set the date and time for examination and request a room for the examination.
      • Begin preparation of the written proposal. Share copy of proposal with committee 2 weeks prior to exam.  Allow a few days and then request feedback.
      • Begin practice examinations.
    • Pass the qualifying exam by the end of the second year, effectively the end of August. Exceptions are only granted in unusual cases (e.g., a leave of absence)
    Click here for a detailed description of the qualifying exam process.

  • Advance to candidacy

    Within three months of passing the oral examination, a student must form his or her thesis committee and file an application for Advancement to Candidacy. If there are any incomplete grades, a student may not advance to candidacy. Following Graduate Division approval, a student is officially advanced to candidacy. Students must be registered for a minimum of three quarters after advancement to candidacy before the PhD degree may be awarded.

    Click here for a detailed description of how to advance to candidacy.

Dissertation & committee meetings

  • Goals

    Broadly speaking, the dissertation committee aims to help guide students through their PhD after the oral exam, providing advice on both scientific matters and, especially in later years, career development. However, the dissertation committee also has responsibilities that extend beyond just providing advice once a year. Because the dissertation committee is best informed about an individual student's progress, the program directors and the Executive Committee rely on their input to make decisions concerning requests for extension beyond 6 years, and to simply be aware of any impediments to progression towards the degree.

    And most importantly, the dissertation committee decides when a student can graduate. More on this below.

  • Timeline

    One dissertation committee meeting is mandated every 6 months. The first dissertation meeting will take place six months after the qualifying exam and then repeat every six months until graduation. Students sometimes seek to postpone the committee meeting so that they can obtain 'one more piece of data'. Don't. Just have the meeting. It's always worthwhile. As with qualifying exams, it is critical to begin scheduling thesis committee meetings 2+ months in advance. As of December 2017, the graduate program will begin to administer dissertation meeting scheduling and will work to confirm meeting dates with your committee on your behalf.

    More frequent or additional meetings may be required by the Executive Committee in cases where it has concerns about progress, or, towards the end of the PhD, e.g., for students requesting extensions to the "6 year rule." Students can also request more frequent or additional meetings if, e.g., their project is at a crucial juncture, they are considering significant changes in direction, or otherwise need advice from the committee.

  • Procedure

    1. Students and faculty should expect meetings to require approximately 90 minutes.
    2. At the outset, the student is asked to leave the room, largely so that the student's primary advisor can briefly update the other members of the committee on progress and any issues from his/her perspective.
    3. The student returns and outlines his/her goals for the meeting, which should generally include feedback on both science and career goals; the balance between these two generally evolves over time.
    4. At some point during the meeting, it is often helpful to present a timeline (as realistic as possible) with your goals for the next year and beyond.
    5. At the conclusion of the discussion, the student should summarize the major points of feedback from the committee; be sure to capture these points in writing.
    6. At this point, the student’s primary advisor is asked to leave, and the student is given the opportunity to bring up any additional issues that, for whatever reason, they feel more comfortable discussing without the advisor present. Sometimes this takes 30 seconds, sometimes longer.

General Guidelines

  • The committee members are responsible for following up on any significant issues with the student's advisor and/or the graduate program director, with the student's knowledge.
  • More broadly, if the committee has significant concerns about a student's progress, it is critical that the program director or manager is informed; the concerns should of course also be communicated to the student and the student's advisor during the committee meeting. These concerns could include: concerns that the student is insufficiently committed to the project, i.e., not putting in enough time in lab, long unexplained absences, etc.; concerns that a dedicated student is not making progress because of potentially insurmountable scientific challenges; or any number of non- scientific issues that interfere with progress. Whatever the case, the graduate program needs to know about it, early enough that the problem can be addressed proactively. The Executive Committee doesn't want to hear about a major issue for the first time when they are asked to approve an extension to the '6 year rule', or when a problem has gotten serious enough that it becomes unclear whether the student will be unable to complete the PhD.

Guidelines for Research Discussion

  • Scientific feedback can be broad, i.e., presenting your progress in general, but it is often helpful to solicit specific advice concerning challenges you have encountered. Or you may wish to present an outline of a manuscript that you are preparing, along with key figures, for feedback and advice about how to improve, where to submit, etc.
  • Your aim should not be to impress the thesis committee (it is not a continuation of the oral exam) but rather to solicit specific feedback to help you move forward. As such, formal presentations, especially with large numbers of slides, are unhelpful; similarly, there is generally no need to extensively review data that has already been published.
  • The committee meeting should be a focused discussion; you have the undivided attention of 3 very smart faculty … don't waste it.

Guidelines for Career Discussion

  • Discussion of career goals is strongly encouraged at all thesis committee meetings, and especially towards the end of the PhD. Thesis committees can be wonderful sources of help in planning the next steps of your career, whether it involves choosing a postdoctoral laboratory, searching for a job in industry, or exploring career options.
  • Students should include such topics in their list of goals for the meeting, and ensure that sufficient time is available, i.e., to ensure that the discussion is not pro forma or rushed, squeezed into the last 5 minutes of the meeting.
  • Students are strongly encouraged to utilize Individual Development Plans to guide the discussion of their long- and short-term goals. At this time, the NIH does not prescribe any one IDP format, and we encourage students to choose one that they find most useful. Two widely used IDP forms can be accessed on the UCSF Office of Career and Professional Development website (both have UCSF connections; one was developed by former Tetrad student Cynthia Fuhrmann). Simply fill out the forms and bring copies with you to provide to the thesis committee; it is probably best for students to discuss the contents with their advisor(s) in advance.

Student Retreat Talks

Goals

  • To provide students with an opportunity to improve their presentation skills.
  • To serve as a formal milestone in the long interim between passing the oral exam and graduating, with the student presenting their progress to the entire student body as well as certain faculty.

Guidelines

  • Depending on timing of the retreat and other factors, students at the end of their 4th year or in their 5th year will be asked to speak.
  • The student’s thesis advisor should make every effort to attend.

  • Graduation

    General principles

    • Obtaining a PhD from UCSF signifies that a student has demonstrated the ability to perform and complete high-quality research that makes an original contribution to their field. In practice, the expectation in Biophysics is that at least one first-author paper is "in press" before the thesis is signed. Learning to respond to reviewer critiques is a critical part of graduate training. There is, however, no simple bureaucratic formula to determine what is sufficient, and often the body of work forming a thesis is reported in multiple first-author publications; there are way too many scenarios, and so we rely on the judgment of the thesis committees to make the evaluation of a substantial and original contribution to science.
    • As discussed above, the dissertation committee has broad authority to determine when a student has completed a sufficient body of scientific work to graduate, literally by 'signing off' on the thesis. In rare cases, the Executive Committee and the program director may become involved in the process, e.g., if the student and his/her advisor do not agree on when it is appropriate for the student to graduate.
    • In no case is it acceptable for a student to ask their committee to sign their thesis solely because they have accepted a job or wish to 'move on' for one reason or another. The degree will not be granted until the dissertation committee is satisfied that the requirements for graduation have been met, e.g., by completing the publication process for a critical portion of the dissertation, regardless of whether the student remains 'in residence' at UCSF.

    Deadlines & procedures

    • Students are expected to complete their PhD within 6 years, not counting approved leaves of absence. Exceptions can be granted only by the Executive Committee. Generally, the Executive Committee has been inclined to grant approvals for 3-6 month extensions in cases where the student, the advisor, and the other members of the dissertation committee all agree that the additional time is warranted, most frequently in cases where the student is completing an ambitious project.
    • The Executive Committee has broad authority to set expectations and requirements for the extension, which may include holding dissertation committee meetings (or meeting with the Executive Committee itself) prior to or after approval. Requests for a second extension, beyond an initially granted 3-6 month extension, are subjected to a higher level of scrutiny. In no case will extensions be granted that would cause the total time- to-degree, excluding leaves of absence, to exceed 7 years.
    • Upon approval from the dissertation committee to graduate, the student must contact the program manager for next steps to insure proper off-boarding.
    • The written dissertation must be provided to faculty several weeks before they are asked to ‘sign off’, to give them time to review it and provide feedback. Generally, faculty will focus on portions of the thesis that have not yet been subjected to peer review, or any aspects on which the student requests feedback.
    • The submission of your electronic dissertation is the final step in the awarding of your degree. The finished document is a scholarly work, and something to be proud of — the result of a long period of preparation and research. Allowing enough time for all the required steps, paying attention to deadlines, and adhering to the format guidelines are crucial. Follow these guidelines carefully to ensure the process goes smoothly. The electronic copy of your manuscript, which you submit to the Graduate Education and Postdoctoral Affairs Dean’s Office through ProQuest, is deposited in the UCSF Library and eScholarship and becomes an official and permanent record available for use by other scholars and the public. Your committee will guide you in the content of your manuscript, and your graduate program may specify certain elements of style in addition to the prescribed format for all programs.
    • While not required by the University of California, it is highly encouraged and customary for students to present a Dissertation Seminar. While the tone is frequently (and appropriately) informal and celebratory, the student should present their scientific accomplishments in a scholarly manner.