Progression Guidelines

From first year to graduation: guidance on bioinformatics student progression

Our goal is for all students to successfully complete their PhD. Formal policies are documented on the GEPA website. This page expands on those policies with guidelines and advice for Bioinformatics program students and faculty. 

Academic advising

First year

First-year students are assigned academic advisors at the start of the year. Academic advisors assist first-year students in exploring rotation and curriculum options. First-years are required to meet with their academic advisor prior to the start of classes and again prior to the Winter and Spring Quarters. Academic advisors have deep knowledge of UCSF and the Bioinformatics program, but their research may not overlap with students’ research interests.

Second year

Academic advisors are available to assist second year students in their preparation for the qualifying exam including brainstorming ideas for committee members. Preparation for the qualifying exam should be guided by the student’s research advisor and exam committee. Second years are encouraged to meet with their pre-assigned academic advisor once at the start of the second year to discuss the qualifying exam.

Third year and up

Students’ main sources of advising in the third year and beyond are their research mentor and PhD committee. Students will meet roughly every six months with their PhD committees to provide updates on progress and get feedback. Meeting with the academic advisor is encouraged but optional. The academic advisor can help with the selection of PhD committee members and can provide an outside perspective on any issues that arise in the lab or program. 

Qualifying exam

Goals

The goal of the qualifying exam is to demonstrate via writing and discussion that the student:

  • Can pose a significant scientific question. 

  • Can apply knowledge of bioinformatics, computational biology, and statistics to cutting-edge problems. 

  • Can develop a systematic approach to its solution that incorporates rigorous study design and statistical analysis. 

  • Can interpret the possible results of that approach concisely and rigorously. 

  • Can identify alternative strategies if the proposed approach fails.

  • Can frame that interpretation both within the context of the relevant literature and of other related biological systems. 

Students should propose the work they want to complete for their dissertation, not a 'hypothetical project'.

 

The scope should describe a focused inquiry with 2-3 related, but non-dependent specific aims. It should not necessarily include all the work that will be done during the PhD. In other words, the proposal should not be a wish-list of everything the student might hope to accomplish, but a focused inquiry that would lead (roughly speaking) to 2 or 3 significant papers.

 

Further guidance for orals preparation is provided to students during second year cohort meetings.

Qualifying Exam Deadline

Second year students must complete the qualifying exam April 15. Committee members must be confirmed by December 31. Exceptions are only granted in extreme cases (e.g., a leave of absence). Inability to schedule committee members is not grounds for an extension. If a potential committee member is difficult to schedule, replace them.

Composition of the qualifying exam committee

The qualifying exam committee consists of four faculty. The committee cannot include your advisor or co-advisor.

 

Adjunct faculty or faculty from other universities can be approved by petition found in the student portal.

 

At least two of the faculty must be members of the Bioinformatics program (at least one must be a core member).

 

The chair of the committee must be a BMI faculty member. Chair responsibilities include: moderating the exam, providing feedback to the student and advisor, and communicating with GEPA and the program administrator.

 

The committee must be confirmed by December 31. When the committee is confirmed, email the program directors and manager (cc:ing all committee members). 

Qualifying Exam Format

The exam has both written and oral components.

 

Written Proposal:

Follow the NIH F31 Proposal guidelines:

  • Specific Aims: 1 page

  • Research Strategy: 6 pages (including figures)

  • + additional pages for references

  • Font: Arial 11 point

  • Margins: 0.5 inches

Here is a link (TBA) to a template with proper formatting and helpful advice. 

 

Submit final version to committee two weeks* in advance of the exam. (*Unless you agree on a different deadline with your committee.) You should get feedback on the written proposal as you develop it from your advisor and committee members. Ask them how and when they would prefer to give you feedback.

 

We hope that following this format will help students submit their proposals for the NIH F31 and/or other graduate student fellowships.

 

Oral Exam:

The goal of the oral component of the exam is to have a scientific discussion that assesses the feasibility and significance of the proposed PhD project and the student's ability to carry it out.

 

The format is a 2-hour chalk talk with no slides. Prior to the exam, the student may write an outline of their proposal on the board to guide the initial discussion, but the talk must be interactive. Be sure to book a room with a large whiteboard!

 

Approximate schedule of an exam:

  • Faculty Discussion (10 minutes): Discussion of administrative details and the proposal without student

  • Introduction to the Project (5 minutes): The student presents an overview of their major goals/hypothesis/questions of the project and the aims proposed to address them. Faculty are asked to refrain from asking questions during this introduction.

  • Project Discussion (1.5 hours): The student presents the details of their approach at the board and responds to questions about all aspects of the project and necessary background knowledge.

  • Faculty Discussion (10 minutes): The faculty will ask the student to leave, so that they can discuss the presentation and come to a decision about the outcome of the exam. It is possible that the committee may decide to ask the student more questions after their discussion.

  • Student Feedback (5 minutes): The committee communicates the outcome and gives feedback to student on their performance and next steps. The chair will follow-up with the student and their advisor by email. 

Outcomes

There are three possible outcomes of a qualifying exam:
 

  • Pass – The committee was convinced that the student is prepared to carry out research in their proposed topic area. Now it is time select a PhD committee (see below) and advance to candidacy (see form in student portal). 
     
  • Conditional pass – In a conditional pass, the committee was convinced that the student is generally ready to carry out the proposed project. However, during the exam, they identified a specific area that needs to be addressed before the student is fully prepared to carry out their research. In this situation, the student will formally pass the exam only after having satisfied a specific condition stipulated by the committee to address a gap in knowledge or capability. The chair of the qualifying exam committee is responsible for evaluating whether the condition has been met, and then signing a 'pass' at that time. However, other committee members can be designated as responsible for evaluating the condition. 

    The condition must be specific and have a clear measurable definition of completion. The condition must also have a realistic timeline, e.g., three months but preferably shorter. For example, “understand machine learning” is not an appropriate condition, but rewriting a specific aim in response to the committee’s critiques is. The committee may also require that the student form their PhD committee and hold their initial PhD committee meeting earlier than normal (e.g., within 3 months). This happens when the student is considered well-prepared, but the committee believes that they would benefit from additional discussion of study design, prioritization of experiments, or other scientific issues that are the purview of the PhD committee.
     
  • Fail – A fail occurs when the student has insufficiently demonstrated their ability to carry out the proposed research. This result from fundamental flaws in the proposed project, insufficient understanding of the background knowledge necessary for the project, inability of the student to describe and defend their approach, or any combination thereof. In the case of a fail, the committee chair is responsible for documenting in writing the committee's concerns and promptly (within one week) sharing them with the student and their advisor. Per university policy, students can take the oral exam a second time. The second exam must occur at least three months after the first exam and must have the same committee. The second exam will follow the same proceed and expectations as the first exam, but the student must pass to continue in the PhD program.

Preparing for the exam

While the qualifying exam takes place over two hours, the outcome is determined over the months before the actual exam as the student brainstorms and refines their project ideas in collaboration with their advisor, lab, committee, and cohort. Meeting with committee members multiple times is critical for success. 

  • Concept – The research question and approach should be developed by the student in collaboration with their advisor(s) and committee, generally starting early in the 2nd year. This process should coincide with starting to carry out the research. Extensive preliminary results are not required, but making progress on the project will help you discuss strengths, weaknesses, and details.

  • Writing – Students should familiarize themselves with the required format and start writing early. The template is structured to provide clear guidelines on what should be described in each section. Seeking out example proposals from previous students and from successful F31 applications is very helpful in providing examples to work from.

  • Committee – The committee must be finalized by December 31. Schedule a preliminary 1-on-1 meetings with possible committee members in the Fall Quarter. When reaching out to potential committee members, students should provide a short description of general project area (or draft specific aims) and explain why the faculty member would be a good fit for the committee. When first meeting with potential committee members, the student should evaluate their engagement and ability to provide constructive feedback and ask about their expectations for qualifying exams. Once the committee is finalized, we strongly suggest meeting with each committee member at least twice as the proposal is developed. 

  • Practice – Chalk talks are challenging. To be successful, students must practice MANY times. In addition to practicing by themselves and with their lab, we suggest attempting to construct a mock committee of trainees from the labs of committee members.

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.