Qualifying Examination

To be eligible to take the qualifying examination, students must pass all of their core curriculum with a grade of B or higher.

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.