Advancement to candidacy

Within six 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.

Thesis Committee Composition

• The committee consists of three members; four if jointly advised.
• The PI is a member of the committee but will not serve as chair.
• Chair of the committee must be a member of the BMI faculty (core or affiliate)

PhD committee meetings

Goals

The PhD committee has multiple responsibilities. The committee helps guide students through their PhD after the qualifying exam by providing advice on scientific matters and, especially in later years, career development. Most importantly, the PhD committee decides when a student can graduate. Program leadership and the Executive Committee also rely on the PhD committee to provide guidance and feedback when making decisions about student progression (e.g., degree extensions beyond six years) and conflicts with advisors.

Timing

PhD committee meetings should be held every 6 months. The first thesis meeting will take place six months after the qualifying exam, unless otherwise specified, 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. The graduate program administers PhD 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 dissertation committee (it is not a continuation of the qualifying 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 dissertation committee meetings, and especially towards the end of the PhD. Dissertation 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 PhD committee; it is probably best for students to discuss the contents with their advisor(s) in advance.

Student Research in Progress Talks

Goals

• To provide students with an opportunity to improve their presentation skills.
• To serve as a formal milestone with the student presenting their progress to the entire student body as well as certain faculty.

Guidelines

• All students in year two and above present their research annually at the weekly Student Research Seminar (BMI 222).
• The student’s PhD 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 Bioinformatics is that at least one first-author paper is "in press" before the dissertation 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 dissertation 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 thesis 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 thesis committee is satisfied that the requirements for graduation have been met, e.g., by completing the publication process for a critical portion of the thesis, regardless of whether the student remains 'in residence' at UCSF.

Deadline and 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 thesis 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 thesis 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.
• The written thesis 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.
• While not required by the University of California, it is highly encouraged and customary for students to present a Thesis Seminar. While the tone is frequently (and appropriately) informal and celebratory, the student should present their scientific accomplishments in a scholarly manner.