Graduate Group in Genomics and Computational Biology

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Thesis Phase

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Thesis Research and PhD Mentorship

The GCB program is designed to provide mentorship and develop skills that will produce independent research scientist in the field of genomics and computational biology.

It is the responsibility of the advisor and the thesis committee to evaluate the scientific quality and importance of the student's work and to decide at which point the student will receive permission to write the thesis.  It is expected that the body of work accomplished is relevant and important to the scientific community.  This criterion can be met by having at least two first author papers published or "in press" in peer-reviewed scientific journals.  Our program is highly interdisciplinary and it is expected that while some students will gain a balanced training in experimental, computational, and statistical areas, others may master a specific field (in genomic or computational biology) but, at the same time, develop competence in the other areas.  In other words, a student with a strong background in one area (genomics or computational biology) should develop skills that will facilitate productive interactions with investigators in other fields.

Thesis Committee

The purpose of the Thesis Advisory Committee is to provide objective advice and fresh points of view to the student and Advisor. A lively discussion may be expected at these meetings, which is sure to benefit the student and his or her research. Committee meetings are also important for ensuring that the student is: i) on schedule to complete his or her Thesis in an appropriate time frame, including maintaining the appropriate balance of experiments, analysis, writing, and dissemination; ii) thinking about and effectively pursuing post-graduation career plans; and iii) at the appropriate time is given permission to write and defend the thesis.

Committee composition. The student should work closely with his or her advisor(s) on the composition of the Thesis Committee.  The committee must include the advisor/co-advisors, a Chair, and at least three other members, one of whom must be external to Penn/CHOP/Wistar.  Students should aim for diversity of field of expertise and gender in their committee.  Once the committee members are selected, they must be approved by the Graduate Group Chair.

Scheduling. The first Committee meeting should take place by the end of the December after the student passes the Candidacy Examination. Subsequently, the Thesis Committee should meet at least once per year to review progress and make plans for the coming year. These meetings typically take place in the Spring semester. As the Thesis nears completion, it is often desirable to meet at shorter intervals.

Because it is challenging to schedule any meeting that includes multiple individuals, please schedule all Thesis Committee Meetings two to three months in advance.  It is very important that all committee members are present for the meeting (members who are on sabbatical can join in using Skype or other videoconference technology).  If more than one member is unable to be present in person, the student should find another time for the meeting.  Students should plan for and expect the meeting to last 2 hours. If finding/confirming a time is difficult, the graduate group coordinator can help with scheduling and finding a location.  Students should first find a set of times that work for the advisor, and then work with the rest of the committee to find a mutually agreeable time.  Many students find Doodle.com to be useful as a scheduling tool.  As soon as the meeting is scheduled, the student should inform the grad group coordinator. 

Meeting Materials. For each meeting, the student must provide:

Meeting agenda. First, the student will leave the room so that the Committee may consult with the Advisor regarding progress and any concerns. Second, the student will return and the Advisor will leave the room so that the Committee may consult in a similar manner with the student. Third, the student then gives a prepared presentation of their progress to date plus plans for the coming year. After the student’s presentation, the committee and advisor should again dismiss the student to discuss his or her progress before conveying their report to the student.

Meeting Report. The Chair of this Committee will provide a brief written report, using the Thesis Committee Meeting Evaluation Form, summarizing the results of each meeting. This form should be filled out at the end of each Committee Meeting, reviewed with the student and then provided to the coordinator.  If Permission to Write was granted, the Advisor and Chair will sign a separate form and give it to the coordinator. 

Permission to Write and Defend the Thesis

The Graduate Group requires a dissertation to represent a definitive contribution to scientific knowledge and to show that a student possesses the ability to perform independent research. The main information contained in the dissertation should be of a caliber sufficient for publication in a reputable, refereed scientific journal.

Before beginning the process of writing and defending his/her thesis, the student must convince the thesis committee that thesis research is substantially finished and that the thesis is ready to be written. If the committee agrees that the experimental work is sufficiently complete and defensible, the "Permission to Write" form must be signed by the committee chair and thesis advisor and returned to the Graduate Group Office. The committee should also agree on a time line that includes an approximate date for the defense. This is necessary to ensure that a time convenient for all committee members can be arranged and that an appropriate room can be scheduled.

The written document must conform to the dissertation rules of the University (see the Dissertation Manual issued by the Office of Graduate Studies). The mentor must be satisfied with the written document before it is distributed to the committee. A draft of the thesis must be presented to each committee member and the GCB office no later than two weeks prior to the scheduled defense. Failure to do this may result in cancellation of the scheduled thesis defense.

The Thesis Presentation and Defense

The thesis presentation will take the form of a public lecture. The lecture should be scheduled well in advance so that a time convenient to the entire committee can be found and notices can be sent to the faculty and student membership. The Graduate Group Office needs to know the defense date, title of the thesis and place and time of the defense at least three weeks in advance. The Graduate Group Office will then send a public notice to the University community advertising the thesis defense. The Graduate Group Office is responsible for the forms which are required after the thesis defense.

Every effort should be made to have the full four-member thesis committee present at the thesis defense. If a thesis committee member cannot be present at the defense, he/she may provide to the committee chair approval of and/or comments concerning the thesis prior to the defense. If that is not possible, the student is responsible for finding a substitute committee member, with the approval of their program chair. Following general questioning during the public phase of the presentation, the thesis defense will commence. The defense is open only to the thesis committee and mentor. The decision on approval of the thesis will be made solely by a majority vote of the committee. The student should anticipate that the committee may require changes to the thesis that could include additional writing, editing and re-evaluation of data. Such changes must then be approved by the committee before the thesis is deposited. For this reason, it is imperative that thesis defenses be scheduled no later than two weeks before the University deadline for depositing theses.

Before a student makes the appointment to deposit the thesis, the student must provide the Graduate Group Office with a copy of the abstract page, an original signed copy of the title page, and a mailing or email address where the student can be reached after graduation. The Graduate Group Office will then provide the student with a signed 153 form, which must accompany the dissertation to the Graduate Division of Arts and Sciences (GAS).


Graduation Procedures

The Graduate Division of Arts and Sciences sets three graduation dates each year in May, August, and December. A formal commencement ceremony is held in May. The Graduate Group Office will distribute a calendar for each degree period, giving the deadlines for signing up for graduation, and for defending and depositing the thesis. If a student is not able to graduate after they have signed up, they must re-apply for the next degree period. The graduate Group Office will guide students through the thesis submission and graduation scheduling.


Recertification Procedure

University rules govern the time a graduate student may take to complete requirements for the Ph.D. In GCB, after initial certification that the student has passed all course work and required preliminary exam(s), the student will have five years to complete: 1. the thesis, 2. the thesis defense, and 3. submission of approved thesis.  Students who have not completed all three requirements within 5 years of first registering for dissertation tuition, will cease to be Ph.D. candidates unless they pass a Recertification Exam.