Graduate Group in Genomics and Computational Biology

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The Candidacy Process

Qualifying Review | Oral Candidacy Exam | Written Proposal Guidelines | Oral Proposal Defense | Timetable for Submission of Proposal | Role of Thesis Advisor | Composition/Duties of Committee | Exam Procedure | Possible Outcomes

Qualifying Review

Each student’s academic record will be reviewed prior to the oral exam. Students are expected to have a 3.0 GPA and no grade lower than a B in the required “core” courses plus their chosen “Approach” and “Biological” Specialty electives. Any grade below a B in these courses may need to be retaken. In some cases, the Advising Committee may recommend a substitute course instead of a retake.

Oral Candidacy Exam

The Candidacy Examination consists of 2 parts: a written Proposal describing plans for the thesis project, and an oral Defense of that document. If there is not a well-developed thesis project by winter of the prelim exam year, the proposal can be focused around any problem central to the work in the thesis lab.

Guidelines for the Written Proposal

The proposal guidelines closely follow those for a Predoctoral Fellowship application to the NIH (NRSA F31). Thus, students should craft their proposal with the following section headings, using single spaced, 11 point Arial font, 0.5 inch margins, and the indicated page limits.

There is no expectation that extensive preliminary data should exist, but if it does, present it within the Research Strategy section (remaining within the 6 page limit). For example, such data might be included as part of the rationale or justification for a particular approach. Any preliminary work that represents unpublished data of others from the thesis lab should be explicitly approved by those providing such data and be properly cited.

The emphasis of the proposal should not be on a review of the literature but on dealing creatively with the problem selected. The proposal should be "hypothesis-driven". That is, it should aim explicitly to address a working hypothesis regarding an unresolved issue in Genomics and Computational Biology. It is important to remember that the proposal should describe work that can reasonably be done by one person in 3-4 years, not what an entire lab of people could accomplish in 3-4 years. In this respect, the written Proposal will be more focused than a mentor’s NIH R01 application. This proposal is only a starting point for the actual thesis work. The approaches and experiments can reasonably be expected to change over time with input from the Thesis Advisor and the Thesis Committee.

Oral Proposal Defense

For the Proposal Defense, there is an expectation of substantial depth of knowledge in the thesis area, broadly defined. Thus, it will not be sufficient to defend only the particulars of the proposed experiments. A key element of the oral examination will be to explain and defend the importance of the questions to be addressed, and to place these questions in the broader context of the field. Thus, in both the Significance section of the written Proposal and in the subsequent oral Defense, the student should be able to marshal knowledge from the relevant literature and from broader areas of Genomics and Computational Biology. Each student's performance will be evaluated on: 1) quality of the written proposal; 2) quality of the oral presentation; 3) defense of the proposal; and 4) general knowledge of computational biology, their Approach, and their Biological Specialty (covered in coursework).

Timetable for Submission of the Preliminary Exam Proposal

Requests to delay or defer the preliminary examination are strongly discouraged; however, such requests will be considered by the Graduate Group Chair in consultation with the student's advisor.

Role of Thesis Advisor

The student is encouraged to consult with their Thesis Advisor during preparation for the Candidacy Examination. The student is also free to consult with any other faculty, students, or postdocs as they develop their ideas. Thesis advisors should not give copies of current or former grant applications to students nor should they edit the student's written proposal. It is the Thesis Advisor's responsibility to ensure that the overall objectives of the proposal are worthwhile. The student can discuss potential experimental approaches with his/her advisor or others.

Composition and Duties of Examination Committee

The Prelim Committee Chair, or his/her Designate

Ideally, the Prelim chair should be present at all exams. The purpose of the Prelim Chair’s presence on the committee is to be able to compare all the exams with respect to rigor and the decision making processes of the different exam committees. With this information, uniformity in decisions can be established. The final decision for each exam (pass or fail) will be made by the Prelim Chair, and then made known to the student by the Graduate Group Chair after all exams are completed. In making these final decisions, the Prelim Chair, will consider the committee's recommendations along with the comparative rigor of all the exams. The Prelim Chair will be responsible for the evaluation forms that constitute the written record for the exam.

Experts

The remainder of the committee will be chosen by the Prelim Chair and will consist of three faculty members with a reasonable degree of expertise covering Core Knowledge and the student’s chosen Approach and Biological Specialty. They should be selected to provide a balance between junior and senior faculty.

Thesis Advisor

The Thesis Advisor is explicitly excluded from being on the Preliminary Examination committee for their own student and has no role in determining the composition of the committee.

Exam Procedure

Prior to the Day of the Exam

As indicated in the timetable for preparation of the preliminary exam proposal, each student will provide each member of his/her committee with a copy of the proposal. In addition, the GCB office will provide a copy of the student's file to each examiner. Faculty should read and review both of these documents prior to the exam. Any problems with the submitted proposal should be held for discussion at the committee meeting.

On the Day of the Exam

The Prelim Chair will serve as the chair of each examining committee or should ask one of the other members to take on this role. Examinations will be scheduled to allow 1.5 hours for each exam. When the committee has gathered and the members have been introduced to the student, the chair should ask the student to leave the room briefly. The topics to be discussed in the student's absence are:

The student will then be invited to return to the room. The chair should explain the ground rules to the student and ask the student to begin the presentation. The student may prepare a 1-2 page handout for members of the committee if a complex diagram is needed for the oral presentation. With the exception of this handout, the student will be expected to use the whiteboard if needed. If questioning is slow in getting started, the committee chair should lead off by asking a question. The chair should then turn over the questioning to one of the other examiners. In a rotating fashion the other examiners should question the student.

Exam questions should be designed to probe the student's depth of knowledge on the subject of the proposal, both theoretical and technical. In addition, exam questions should determine the student's general knowledge, especially as it relates to lecture and seminar courses taken and independent study and rotations completed. Special emphasis should be placed on questions designed to elicit the ability of a student to describe how an experiment was or will be done and to interpret it appropriately. When the chair feels that the student has been examined sufficiently, he/she will ask the student to leave the room while the committee discusses the performance. Each student's performance should be evaluated in four areas: 1) quality of the written proposal, 2) quality of the oral presentation, 3) defense of the proposal, and 4) general knowledge of computational biology, their Approach, and their Biological Specialty. Each faculty examiner will be asked to fill out a form providing a numerical assessment of the performance in the four areas on a 1 to 9 scale according to the NIH scale (1 = superlative to 9 = unacceptable). Additional comments can also be added. These should include an assessment of the student's perceived strengths and weaknesses. These signed forms are returned to the Prelim Chair at the end of the exam. They become part of the student's file. The student will be informed that the outcome of the exams will be made known at the end of the exams for the program. In most cases this is within a few days.

Possible outcomes

Pass

This is the outcome for most students. It can represent a range from absolutely stellar performance to a good, generally solid one. It is appropriate to give a pass when the performance is good, but not perfect, and perhaps was not all that the examiners think the student might be capable of doing. All four aspects listed above should come into play in the discussion, and a very strong performance in one area may serve to offset a weak performance in another area.

Conditional Pass

This is the outcome for students who do well, but perhaps exhibit a significant weakness in a specific, single area. For example, an excellent presentation, oral defense and impressive fund of general knowledge in the setting of a written proposal that is significantly below average could lead to the recommendation of a Conditional Pass. In the event of a "conditional pass" recommendation, the committee must suggest to the Graduate Group Chair what the student should be required to do to address the deficiency (such as rewrite the proposal, do an independent study, etc.) If the student is expected to consult with the committee members individually, this should be stated, and a time frame for completing the remediation should be established. This should typically take less than one month. It is important for the committee chair to put this in writing so that there is no ambiguity about what is being asked of the student. At the end of all the exams the Graduate Group Chair will evaluate and compare all Conditional Passes to make sure they are fair decisions and to assure that the proposed remedial action is equitable from student to student. When the Chair communicates the outcome of the exams, he/she will discuss the conditions of a conditional pass with the student involved.

Failure

This is the outcome when either the written proposal or the performance on multiple aspects of the exam are completely unacceptable. If the overall performance of the student was weak, or if there were significant deficiencies in more than one of the areas being evaluated, the student will fail the exam. Students who fail the Candidacy Exam will be told why in the most specific terms possible. A student who fails will get a chance to rewrite the proposal and defend it at another oral examination.The possible outcomes for the second exam are Pass or Fail. A student who fails the exam twice must leave the program and has the option of obtaining a Terminal Master's Degree.