For PhD Candidates

Forming your thesis committee

Purpose of your thesis committee is to evaluate your scientific progress and to suggest directions in research that will culminate in a successful thesis. Your committee as a whole, and as individual members, should be willing as well to help in other facets of the your scientific and professional development.
You should begin forming your thesis committee after passing your candidacy exam.
Your committee should be set no later than the end of August, so you can have your first meeting by December.
Your committee should consist of a Chair and at least three other members, one of whom must be external to Penn/CHOP/Wistar.
The Chair must be Associate Professor level or higher and must be a member of GCB. At least half of the committee must be members of GCB.
You should aim for diversity of field and gender.
When your committee is formed, please email the graduate group chair and coordinator for approval.

Choosing your thesis chair

The thesis chair plays the primary role in ensuring that your committee meets all of their responsibilities.
The chair will also communicate any concerns about your progress/plans or student-advisor interaction to the graduate group chair.
The chair prepares the Thesis Committee Meeting Evaluation report and distributes it to your committee, to you, your advisor and the coordinator within one week after your meeting.
Your thesis chair must be of Associate Professor rank or higher and a member of GCB.
It is helpful to have a chair who has served previously on thesis committees or who has had multiple grad students of their own.
Your chair cannot have a close collaboration with your advisor.

Scheduling

Because it is challenging to schedule any meeting that includes multiple individuals, please begin scheduling your first meeting as soon as your committee is formed. It's best that you get the date on the calendar before holiday break in December.
It is important that all committee members are present for the meeting (members who cannot be present for an in-person meeting can join in via Zoom, etc.). If more than one member is unable to be present, you should find another time for the meeting.
You 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. You should first find a set of times that work for your advisor(s), and then work with the rest of the committee to find a mutually agreeable time.
Many students find Doodle to be useful as a scheduling tool.
As soon as the meeting is scheduled, inform the graduate group coordinator, who can help you reserve a room.

Meeting Materials

Individual Development Plan

You and your mentor should meet in the two weeks prior to your meeting to discuss and complete the NIH-mandated Individual Development Plan.

Thesis Proposal

Your proposal should be 7 pages and written in NRSA format.
Include Specific Aims and Research Strategy (Significance, Innovation and Approach).
The proposal should clearly describe your novel biological and computational hypotheses.
Send your proposal to your committee and the graduate group coordinator at least one week prior to the meeting.

Presentation

Content of the presentation varies depending on the progress of each student.
You are strongly encouraged to ask fellow students for advice re: the presentation.

Additional requirements

Send your lab notebooks to your committee chair at least a week before your meeting.
Please fill out this form and send it to your committee along with your proposal (form will indicate whether or not you fulfilled your RCR/IDP requirements.)

Meeting Agenda

First, you will leave the room so that the committee may consult with your advisor(s) regarding progress and any concerns.
Second, you will return and your advisor(s) will leave the room so that the Committee may consult in a similar manner with the student.
Third, you’ll give a prepared presentation of your progress to date plus plans for the coming year.
After the presentation, your committee and advisor(s) will dismiss you to discuss your progress before conveying their report to you.
The student is expected to lead the discussion during the thesis committee meeting. The thesis advisor(s) may contribute, but should do so judiciously and only when necessary.

Meeting Report

The Chair of your committee will provide a brief written report, using the Thesis Committee Meeting Evaluation, summarizing the results of each meeting.
This form should be filled out at the end of each meeting, reviewed with you and then provided to the coordinator.
The coordinator will send the evaluation form to your committee chair a week before your meeting.
Please contact the coordinator with any questions regarding the evaluation form.

Scheduling

Your committee should meet at least once per year for PhD students and every six months for Combined Degree students to review progress and make future plans. As the Thesis nears completion, it is often desirable to meet at shorter intervals.
If finding/confirming a time is difficult, the graduate group coordinator can help with scheduling. You should first find a set of times that work for your advisor(s), and then work with the rest of the committee to find a mutually agreeable time.
As soon as the meeting is scheduled, inform the graduate group coordinator, who can help you reserve a room.

Meeting Materials

For each meeting, the student must provide:

Individual Development Plan

You and your mentor should meet in the two weeks prior to the annual thesis meeting to discuss and complete the NIH-mandated Individual Development Plan.

Progress report

Concise written summary (no more than three text pages, plus figures) of progress and future plans.
A copy of the previous Thesis Committee Report, to be provided to the Committee at the beginning of the meeting.
Send your progress report to your Committee and graduate group coordinator at least one week prior to the meeting.

Presentation

Send your presentation to the graduate group coordinator. It can be sent either before or after the meeting.
The student is expected to lead the discussion during the thesis committee meeting. The thesis advisor(s) may contribute, but should do so judiciously and only when necessary.

Lab notebooks used since the previous meeting

In keeping with BGS policy, the Thesis Committee Chair is responsible for ensuring that lab notebooks are reviewed at each meeting, either by one designated committee member or by the committee collectively.
There is no expectation that lab notebooks be reviewed in their entirety. However, the Committee should feel confident that the student's lab notebooks and overall data organization are complete and well managed.
If any concern arises from the lab notebook review, then the Committee will undertake a more extensive review at the earliest possible time after the Committee meeting. If the Committee finds that the lab notebooks are incomplete and/or poorly managed, then they should provide: i) explicit, written and verbal instructions to the student for improving the notebooks, and ii) a deadline for submission of the notebooks for re-review. It must be emphasized to the student that any modifications made to the lab notebooks should occur on separate, previously unused pages on which it is explicitly stated that supplemental notes are being made to a previous (and dated) experiment.

Electronic notebook used since the previous meeting. This should contain:

Clearly articulated statement of purpose.
Use of version control, including snapshots of material (tables, figures) that is part of a publication.
Adequate pipeline annotation: Readme, shell script, etc.
Adequate description of the input data.
Adequate description of the output data and format, using standardized formats where possible.
Description of data/analysis back up procedures.

Previous thesis committee evaluation

A copy of the previous Thesis Committee Evaluation should be provided to the committee at the beginning of the meeting.
Please contact the graduate group coordinator if you need a copy of your previous evaluation.

Additional materials

Please fill out this form and send it to your committee along with your progress report.

Meeting Report

The Chair of your Committee will provide a brief written report, using the Thesis Committee Meeting Evaluation, summarizing the results of each meeting.
This form should be filled out at the end of each meeting and reviewed with you.
If Permission to Write was granted, your Advisor and Chair will sign a separate form and give it to the graduate group coordinator.
Please contact the graduate group coordinator with any questions regarding these forms.

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. The Permission to Write form must be signed by the committee chair and thesis advisor, and then returned to the graduate group coordinator.

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 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 your defense:

Review the graduation calendar dates.
Work with your advisor(s) and committee members to find a mutual date/time.
Inform the GCB coordinator when your defense is scheduled, so they can help you reserve a room if you are having an in-person or hybrid defense; if you are having a fully virtual defense, send the GCB coordinator the link to the Zoom meeting.

Before your thesis defense:

Register online for your degree at: https://srfs.upenn.edu/student-records/GradApp
Consult the Dissertation Manual for instructions on formatting and submitting your thesis.
Submit your thesis title to the GCB coordinator at least one month before the defense date so that the defense can be announced and paperwork can be prepared. Please also send a picture of yourself or your research to be used on the talk advertisement.
When the dissertation has been written, distribute a penultimate draft to your Thesis Committee at least two weeks before the scheduled defense. Thus, before the final draft is submitted, each committee member can identify necessary revisions and suggest improvements.
Make an appointment to deposit your dissertation with the Office of the Provost. 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 grad-degree@provost.upenn.edu to sign up for an appointment. When your appointment is scheduled, inform the GCB coordinator of the date.

After your defense:

Fill out form 154 with post graduation information.

Every BGS PhD and Combined Degree student is required to complete an Individual Development Plan (IDP) on an annual basis. An IDP is intended to help in the design of, and measurement of progress in, training. It is also intended to help in identifying short- and long-term objectives and relevant development activities. Each student should use the IDP that aligns with their progress in the PhD program and status as a PhD or combined degree student. The IDP is due August 1 of each year.

GCB IDP schedule for thesis students:

Meet with your advisor(s) to discuss the IDP either before your next thesis committee meeting or anytime by the August 1st deadline.

IDPs can be found in the Forms section below.

BGS requires all of its predoctoral students to be trained in i) Responsible Conduct of Research (RCR), and ii) Scientific Rigor and Reproducibility (SRR).

Training in RCR is achieved through lecture, web-based programs, small group workshops, and RCR-focused lab meetings. Training places an emphasis on the involvement of faculty and satisfies requirements set by the NIH for individual fellowships and training grants.

Training in SRR is achieved through lecture and SRR-focused lab meetings. Training similarly places an emphasis on the involvement of faculty and satisfies requirements set by the NIH for individual fellowships and training grants.

PhD student requirements

MD-PhD student requirements

GCB encourages students to apply for fellowships and will help with the process. Even though students are fully-funded, the process of applying for a fellowship is valuable, and gives you a taste of what it will be like to apply for other fellowships and research grants later in your career.

Resources:

Please contact the coordinator if you need access to the GCB fellowships folder.
A list of fellowship opportunities can be found here.
The BGS website has helpful information that includes tips for applying.

Information regarding funding, requesting travel funds, taxes, etc., can be found here on the BGS website.

Please contact Anne-Cara with any questions related to the above.

GCB LinkedIn Group
BGS LinkedIn Group
BGS Career Development (can find job postings in Career blog section)
Penn Career Services

Biomedical Graduate Studies

Graduate Group in Genomics and Computational Biology

For PhD Candidates