Thesis
Qualifier:
Students are expected to write and orally defend the Thesis Proposal by September 1 at the beginning of the third year. If the student enters with a Master’s degree, they are expected to write and orally defend the thesis proposal by January 1 of the second year.
The purpose of the Qualifying Examination is to ensure that you have mastered the fundamentals of biophysics relevant to your proposed research and are adequately prepared to begin working full-time on your thesis research. The Exam comprises the preparation of a written research proposal and an oral defense of the proposal to a faculty committee.
The structure of the written document should be similar to NIH F31 grant application and is described in detail below (detailed instructions are also available from the NIH website). You are expected to present the written proposal to your committee members at least one week before the oral defense.
IT IS ESSENTIAL that this proposal presents an original project with original ideas developed and written by the student. While proposals from colleagues, including the student’s mentor, can be used as guidelines, there must be no scientific overlap between your Qualifying Exam written proposal and any other document from either your mentor or other colleagues.
Proposal Instructions:
Your proposal should describe the research plan for one person (you) for a three-year period. It should follow the format of an NIH application with five sections. Remember that in evaluating your proposal, reviewers will be looking for more than just the protocols for your experiments; they will also be looking to ensure that you can explain the rationales behind your experiments, the justifications for their importance, and the possible interpretations of various outcomes. In short, the scientific ideas that are part of a research project are at least as important, if not more important, than the technical methods. Your proposal should contain the following sections. The page lengths indicated are very rough suggestions, but the total length of sections I-IV must not exceed 10 pages.
I. SPECIFIC AIMS (1 page)
First, state your overall objective, concisely and realistically. This objective should describe what the
research is expected to accomplish and what hypothesis is to be tested. Then list the major experimental
goals (i.e. specific aims} that will be completed to achieve that overall objective during the course of your
study.
II. BACKGROUND AND SIGNIFICANCE (1-2 pages)
Briefly describe the background for your proposal, critically evaluate existing knowledge, and specifically identify the knowledge gaps that the project is intended to fill. State concisely the importance of the research described in this proposal by relating the specific aims to longer term objectives beyond the scope of the proposed 3-year study.
III. PRELIMINARY STUDIES (2-3 pages)
Provide an account of any experiments you have already carried out that might be pertinent to the research plan. You may also briefly review the history of the project and relevant work accomplished by others in your lab. If you have not yet started experiments relevant to the proposed project, this section will include more the latter than the former. If the project is new to your lab, this section can be very short. Appropriate figures, graphs or tables should be included, if available.
Do not delay preparing your Qualifying Proposal to accumulate more preliminary results. Your experimental skills at the bench are only one small facet of the exam. The most important consideration is your ability to think logically and present your proposed research in clear and insightful ways. While Preliminary Studies in an actual NIH application, by an independent investigator, would be required to make a compelling case for the proposed experiments, your Qualifying Proposal is not an actual application, nor are you an independent investigator. It is unwise to delay preparing your proposal to get more preliminary results, rather the opposite is true. You will get good feedback from your committee about the design of your experiments. If you are considering delaying your Qualifying Exam beyond the end of the spring semester of your 2nd year, you should speak with the Director of Graduate Studies.
IV. EXPERIMENTAL DESIGN AND METHODS (3-4 pages)
Explain in detail the experimental design and procedures that will be used to accomplish the specific aims
of the project. For standard experimental approaches (e.g. DNA sequencing or ELISA), cite an
appropriate reference for the method; no need to detail experimental specifics. For more specialized methods specific to your project, describe the approaches with sufficient detail to be understood by a reviewer not entirely familiar with your field of research. Discuss how data will be analyzed and interpreted. Discuss the potential difficulties and limitations of the proposed procedures and alternative approaches to achieve the aims.
V. LITERATURE CITED
Use complete literature citations, including all authors and titles. The bibliography need not be exhaustive,
but should be relevant and current.
FORMATTING: The suggested lengths for each section refer to single-spaced text in easily readable type sizes such as Arial 11pt, with at least 0.5 inch margins, as required for NIH format. This is a minimum, all reviewers appreciate adequate spacing in the document, in any case do not exceed a total of 10 pages, excluding Literature Cited. You and your reviewers will probably appreciate liberal use of subheadings, which help organizing the material. For example, if you have three specific aims, you will probably have three major subdivisions if Part IV, and additional subheadings within these. Since this format is essentially that of an NIH grant, it may be useful for you to study examples of these, either from your mentor, your committee members, or other colleagues.
ORAL EXAMINATION: The written Proposal will be presented evaluated by the student’s selected thesis committee. For the Oral examination, the student should present the written proposal in approximately similar format, with the background, justifications, aims of the research, preliminary data and proposed experiments (not necessarily in that order). During the examination, the committee will discuss these aspects with the student to probe the student’s depth of knowledge on relevant topics and ability to think critically about aspects of their Proposal.
The committee may decide to award a full pass, conditional pass, or fail. The committee will provide detailed critiques to the student in order to meet the conditions to fully pass, or to help improve the thesis proposal and the oral defense in the case of a fail. The student must pass the qualifying exam on the second attempt or the program will recommend dismissal from the School of Medicine.
Milestone: PHDCAND
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