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.
BGS developed a set of expectations for thesis mentors, students, and thesis committee members in 2016. It can be found here.
The University has issued an extensive set of guidelines for Advising and Mentoring PhD Students.
Students or faculty with questions or concerns about expectations should contact the graduate group chair or the BGS director.
Thesis committee members can serve a variety of roles in the student’s project. At a minimum, they attend all thesis committee meetings and offer feedback, read and comment on the thesis manuscript, and attend the defense. Often, they serve as informal advisors on the thesis project, and meet with the student as needed between committee meetings. The Committee Chair is specifically responsible for running the committee meetings, completing the paperwork, and submitting it to the GCB office.
The student should work closely with their advisor(s) on the composition of the Thesis Committee. The committee must include the advisor(s), a Chair, and at least three other members, one of whom must be external to Penn/CHOP/Wistar; at least half of the committee members must be members of GCB. The Chair must be of Associate Professor rank or higher, and must be a member of GCB. Adjunct professors may serve on the committee but may not be the committee Chair. 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.
GCB strongly encourages students to be co-mentored by faculty with complementary fields of expertise. This can take a variety of forms, depending on the student’s interests and the faculty members’ needs. Often, students will have a primary mentor, who hosts and supports the student, and a secondary mentor, either formally (e.g. co-authorship, registration on the university level), or informally. Occasionally mentors will split the financial support of the student. Co-mentoring arrangements should be discussed with the GCB office as soon as the secondary mentor is identified.
PhD students should meet with their Thesis Committees at least once per year. For Combined Degree students, meetings should take place every six months. The purpose of these meetings is to provide objective advice and fresh points of view to the student and advisor(s). A lively discussion may be expected at these meetings, which is sure to benefit the student and their research.
Committee meetings are also important for ensuring that the student is:
i) on schedule to complete their 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.
Current students can find more details about thesis committee meetings here.
When a suitable body of research has been completed, the Thesis Advisory Committee is convened. If the committee approves, Permission to Write is granted, and the dissertation writing is begun. After permission is granted, students have six months to complete and defend their thesis. If the student has not finished at the end of the six-month period, another thesis committee meeting must be convened and permission must be reissued.
The dissertation is the document that summarizes the student’s scientific work, stating the objective and question of interest (and/or hypotheses), the previous literature motivating the dissertation work, and the set of approaches, method, analyses, or wet-lab experimental techniques used to bring data to bear on the question. It describes results or data from leading efforts of the student, but can also describe collaborative work as applicable. For collaborative work, it is critical that the student focuses on their contribution while also acknowledges the contributions of collaborators.
The dissertation’s overall organization is up to the student in consultation with the thesis advisor and chair of the thesis committee. It is essential that the student consult with the thesis committee chair and thesis advisor(s) on the structure and organization for the dissertation, and that they approve of a structure and format prior to writing. The written document must conform to the dissertation rules of the University (see the Dissertation Manual issued by the Office of Graduate Studies).
As a guide, GCB recommends the following organization and included chapters for the thesis, based on our experiences of successfully defended, high-quality dissertations that have emerged from our program:
General Introduction: This chapter describes an overall review of the literature and presents background materials underlying the thesis and which form the basis of presented work. This should cover background for all thesis chapters, such that a scientifically-minded reader but perhaps non-domain expert could, after reading the introduction, be able understand and consider critically the subsequent thesis work. Another way to think about this chapter is viewing this as a well crafted review paper which summarizes the extant literature around a given set of topics central to understanding the thesis.
Data and Experimental chapters: These chapters correspond to the experimentally-centered scientific units of the dissertation. Each of these chapters could stand on their own. As such, each can (and often do) require their own sections for:
Introduction: which captures the specific background central to the motivation for the data chapter.
Materials and Methods: which should be complete with sufficient detail such that experimental efforts can be reproduced and recapitulated. Links to programming code housed at external repositories may be necessary, but also may not be sufficient, to cover the contents of this section.
Results: which consist of the completed work, analysis, scientific unit of discovery, and inference made.
Discussion: summarizing the results and placing the work and its inference in context with the extant literature and the potential implications of the findings presented.
Future Directions: This chapter synthesizes the collection of the work presented in the thesis, the major conclusions drawn, and inferences made. The goal of this chapter is not to simply summarize the results from each chapter (that has already been done, above). Rather, this chapter provided the student an opportunity to place the collection of thesis work in context, describe significance, implications, directions for scientific effort, and perhaps even proposals for experiments the thesis student might expect to be fruitful lines of inquiry given their scientific contribution.
References: A collection of references made throughout the thesis (across introduction, each chapter for science, and future directions) are organized at the end of the thesis.
Scheduling the Defense
The student should schedule the defense well in advance, confirm with all members of their Committee, and work with the Graduate Group Coordinator to reserve a suitable location for an in-person or hybrid defense; fully remote defenses are also allowed. When the dissertation has been written, the student is to distribute a penultimate draft to the Thesis Committee at least two weeks before the scheduled defense. Failure to provide a chapter at least two weeks in advance risks cancelling the scheduled defense. Before the final draft is submitted, each committee member can identify necessary revisions and suggest improvements. It is typical for members of the thesis committee to ask for revisions prior to the dissertation’s final submission; such revisions can also be requested at the thesis defense.
After the student has had the opportunity to meet the criticisms and incorporate the suggestions of the committee in a final draft, a thesis defense is held. This defense includes a formal “public” seminar followed by a private session with the Thesis Committee. Following this private session, the Thesis Committee renders its recommendation on granting the degree. All thesis committee members must sign an electronic certification form, which is then submitted to the GCB Chair for final approval. Traditionally, the student’s mentor introduces the student at the beginning of the public defense, and hosts a party after the committee informs the student of its decision.
Students must schedule an appointment to deposit the dissertation with the Office of the Provost; however, this is not a meeting, and the student is not be present when the dissertation is reviewed. The dissertation must be approved by the student's thesis committee before the deposit appointment takes place. Appointments can be scheduled via Calend.ly; students who wish to schedule deposit appointments during peak times (the last three weeks of a term) should email firstname.lastname@example.org to sign up for an appointment. The Dissertation Manual, including templates, and the online application for graduation can be found here and a Graduation Checklist can be found here.
Current students should visit the resources page for more details on the above.