Second-Year Qualifying Examination

The second-year qualifying examination (BQE) is designed to examine the student's ability to think critically, analytically, and independently, and to apply the skills acquired in classes to a real research project. The subject of the exam is the student's current research project, but the focus is the student's critical analytical ability and command of relevant methods and subjects. In this vein, committee members may ask general questions that, while originally prompted by the student’s proposal, are intended to test the student’s depth of knowledge in significant areas of bioinformatics or systems biology.

The exam is normally taken before the completion of spring quarter in the student's second year; however, requirements for the first two years must be completed before or in the quarter it is taken, including core classes, rotations, colloquia, student seminars, and ethics.

The exam consists of two components: a ten page written proposal and an oral exam. One week prior to the exam date, the student will submit a ten page proposal. Both written and oral formats should have the following sections, in line with NIH proposals (page counts are for the written proposal, and will differ for oral presentation slides):

  • Specific Aims: A one page description of specific objectives of the project.
  • Significance and preliminary data: The report must clearly articulate the significance of the proposed activity, and describe preliminary work that illustrates the promise of the approach. We expect this part to be the bulk of the proposal (5-7 pages).
  • Approach: A 2-3 page description of what the student proposes to do to extend the preliminary results and to achieve the specific aims.
  • References: In addition, the proposal should cite, and provide references to, related work in the area. The bibliography is not included in the ten page limit.

The second component is the oral exam, where the student defends their proposal. Again, we expect the student to spend the bulk of the time describing their preliminary data.

For each student, the Program will appoint three Program faculty to form the Second-Year Qualifying Exam Committee, one of whom will serve as chair. The student is responsible for scheduling the exam in the fall, winter or spring quarter of their second year. The student's dissertation advisor is not included in the Qualifying Exam Committee. The student will present a practice talk in the Student Research Talks (BNFO 283).


Please read these links well in advance of your exam: