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Qualifying Exam Procedures

General Description and Timeline

The purpose of the Qualifying Examination is to determine whether the student is qualified and competent to continue work toward a Ph.D. in Biophysics.  It is not intended as a test of the proposed research problem or of the supporting experimental data, but rather as a means of determining the potential of the student for independent thought and his or her comprehension of the general field, as well as the capacity for exploring a relevant problem in a scientifically sound manner.

The timeline for the examination as stipulated by the School of Medicine and Dentistry requires completion before the start of the fifth semester of study.

The Qualifying Examination will be carried out by the thesis advisory committee and a member appointed by the Education Committee Chair who will replace the student’s thesis advisor for the examination.  The advisor will not be present at the examination.

The examination is comprised of written and oral components.  Because a career in science will undoubtedly involve submission and defense of research proposals (whether in an academic or industrial setting) the use of a modified NIH grant proposal format is required as described below.

Students must have completed a minimum of 24 hours of course work credit, as outlined above, at the time of the Qualifying Exam.  The completed qualifying exam research proposal must be submitted to each member of the thesis advisory committee and to the Graduate Studies Coordinator (or proxy thereof) at least 10 business days before the day of the examination.  The coordinator’s copy must be emailed.  Copies for committee members are generally on paper, although an electronic copy is acceptable if requested by the committee member.  The Qualifying Exam must be completed by October 1st at the Beginning of the third year of graduate study. 

Students in the Ph.D. Program in Biophysics receive a "Plan B" Master’s degree after passing the Ph.D. Qualifying Examination.  The number of credit hours required for the "Plan B" Master’s is 30, as described above, of which a minimum of 24 must be course work.

Scheduling Procedure   

  1. Schedule your Qualifying Examination with committee members and the faculty member appointed to the exam committee a minimum of 7-8 weeks prior to the exam.  Once you have polled your faculty for their availability and a date/time/location has been set, all students are advised to get confirmation from the committee members to assure it has been added to their calendars.  The office staff does not send out reminders to your Qualifying Exam committee members.
  2. At least 6 weeks prior to the exam, inform the Graduate Studies Coordinator of the chosen date and time of the exam, confirm with all committee members and schedule a room.  At least 25 business days prior to the exam, submit the title and abstract (30 lines of text maximum using font and margin guidelines in Section IV D) via email to the Graduate Studies Coordinator.  The Coordinator will complete the necessary paperwork and submit it to the Registrar.
  3. Submit a copy of the proposal to each committee member and the Graduate Studies Coordinator a minimum of 10 business days before the exam.

The annual Research Review form cannot be completed at the time of the Qualifying Exam because the Ph.D. advisor is not present.  The Research Review should be completed after the student’s annual seminar.  Note:  The chair of the Qualifying Exam Committee will be appointed by the Senior Associate Dean for Graduate Education.  Although notification of the exam will be sent to committee members by the Registrar, the student is encouraged to remind the committee members by email at least 24 hours prior to the oral examination; provide the time and location.

Guidelines for Preparation of the Written Ph.D. Thesis Research Proposal

  1. Overall area of the Proposal:  Because students will have the most familiarity with the scientific area corresponding to their thesis research, it is expected that the research proposal will be drawn from this area.  However, it need not correspond exactly to the student’s planned thesis goals and experiments.
  2. Preparation and Format:  To provide students with an introduction to the methodology of research proposal writing, the Department of Biochemistry and Biophysics offers a two-credit course (BPH 567) each Spring semester.  Most students in their second year of study are required to complete this course for credit.  As part of the course requirements, students will prepare a research proposal that may serve as the basis for the Qualifying Examination proposal.  The format of the proposal should follow a format similar to an NIH R01 grant application as described below in section D.
  3. Guidelines for Getting Help and Feedback from Others:  Successful scientists rely on communication with their peers to produce the best product possible.  Proposal preparation is often an iterative process of draft writing, evaluation by others, feedback, and re-writing.  However, no scientist can be successful without the ability to independently focus on a research area and the ability to develop a plan of experimentation that solves important problems in that research area.  Thus, it is an absolute requirement that the student alone devises the overall goals of the proposal (the Specific Aims) and that s/he designs the specific experiments to achieve those Aims.  During the proposal-writing course, students will receive extensive feedback primarily centered on writing style and the elements of writing a logical proposal.  Occasionally, a “fatal flaw” in an experiment may be pointed out, or the need for additional justification (or experimentation) will be discussed.  Likewise, students may ask peers and their advisor to provide comments on writing style, logical flow, and details of experimental techniques. 

Qualifying Examination Research Proposal Format

The format of the qualifying exam follows the National Institutes of Health R01 grant application format. Page lengths are based on standard, single-spaced pages.  Use 11 point Arial, Helvetica, Palatino, Linotype, or Georgia fonts with 0.50 inch margins at the top, bottom and sides.  Do not exceed 1 page for the Specific Aims and 12 pages for sections ii-iv, including figures (inserted with figure legends in boxes throughout the text).  A new page with the heading “References” should be included as additional pages, and does not count in the page limits.  No Appendices will be considered.  Guard against plagiarism as described above. Label the top of each page with your name in the header.  Include a centered page number at the bottom of each page.  A face page should be included with: the title of your proposal, your name, the date of the oral exam, exam location, and your Ph.D. advisor’s name.  The face page does not count in the page limit.

Qualifying exam proposals that do not follow this format will be rejected without review, similar to NIH policy.  The qualifying exam will be postponed until the proposal is revised to meet the format requirements.

The pages of the proposal should have the following headings:

  1. Specific Aims:  State concisely and realistically what the research described in the proposal is intended to accomplish including what hypothesis will be tested, or what question will be answered.  Do not exceed one page.
  2. Significance:  Briefly sketch the background to the proposal and critically evaluate existing knowledge, clearly indicating the gaps in knowledge that will be filled by the proposed research.  State concisely the importance of the research described in your proposal by relating the specific aims to longer-term objectives. Students need to state the premise (usually 1-2 sentences), which is the underlying reason why the proposal is important; e.g, It is recommended that the entire section not exceed 0.5-2 pages.
  3. Innovation:  This section should place the proposed work in the context of previous work in the field and emphasize the novel approaches and outcomes.  Describe new methodology and its advantage over existing methodology.  Innovation should also be described in terms of conceptual innovation.  For example, a concept can be innovative but the experimental approach may be standard.  It is recommended that this section not exceed two paragraphs or a series of bullet points on the conceptual or experimental innovation of the proposal.
  4. Approach:  This section should outline the work accomplished by the student and the proposed work.  The qualifying examination is not intended as an assessment of the amount of data the student has acquired.  However, available preliminary data should be included as evidence of feasibility for the proposed experimental plan.  Next, the overall strategy to address the specific aims and the experimental design should be discussed.  Describe the protocols to be used in broad terms, and provide tentative timetable for the overall investigation. A suitable experimental design will describe plans to incorporate scientific rigor and transparency, as well as biological variables as necessary; e.g., see  Include a discussion of the possible results of the proposed experiments and how each result will be interpreted (i.e. state the specific criteria for success).  Discuss the potential difficulties and limitations of the proposed procedures and suggest alternative approaches to achieve the aims.  There is no page limitation for this section, but stay within the confines of the 12 page limit for sections ii-iv and make every attempt to be concise. A statement of Authentication of key biological and chemical resources is not required, but this item should be considered in the experimental design.
  5. References:  Use a standard journal format that includes all authors, the year, the title of the article, the journal, volume and pages numbers.

Oral Qualifying Examination Format

The student is expected to prepare an overview of the thesis research proposal that should last no longer than 25 min.  This oral presentation can be conducted using complementary information placed on a blackboard, transparencies displayed on an overhead projector or a computer linked to a video projector.  The student should anticipate interruptions during the presentation to allow the committee to examine the student orally.  A typical examination will take between two to three hours.  The candidate is judged on: the written and oral presentation, a grasp of the fundamental issues, the ability to apply the background from formal course work to problems related to the proposal, and a demonstration of critical assessment of results.  It is important to recognize that while the written proposal serves as a focus for the oral examination, questions can be raised about related areas.

Results of Qualifying Examination

The Chair of the examining committee or the committee as a whole will discuss with the student the strengths and weaknesses of the qualifying exam performance, and will inform the student whether or not s/he has passed the examination.  The Chair will also report strengths and weaknesses to the student’s thesis advisor, and will report whether the student has passed or failed to the Senior Associate Dean for Graduate Studies of the Medical School and to the Graduate Studies Coordinator, who will inform the Director of Graduate Studies. 

If the student passes pending modifications to the thesis proposal, he/she will be given 14 calendar days after the exam to make the necessary revisions.

In the event that a student fails the examination, the student’s performance will be reviewed by the BSCB faculty and a recommendation will be made to the Senior Associate Dean of Graduate Studies.  The recommendation may be that the student must retake the qualifying examination or that s/he must leave the program.