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 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
  • You should aim for diversity of field and gender
  • When your committee is formed, please email the GG 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 GG 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
  • Helpful to have a chair that 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

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Scheduling 

  • Because it is challenging to schedule any meeting that includes multiple individuals, please schedule your first meeting as soon as your committee is formed. It's best that you the date on the calendar before holiday break in December.
  • It is important that all committee members are present for the meeting (members who are on sabbatical can join in using Skype or other video conference technology). If more than one member is unable to be present in person, 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, 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 GG 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 GG 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 fufilled your RCR/IDP requirements.)

Meeting Agenda

  • First, you will leave the room so that the committee may consult with your advisor regarding progress and any concerns. 
  • Second, you will return and your advisor 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 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 is free to 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 eval form to your committee chair a week before your meeting
  • Please contact the coordinator with any questions regarding the evaluation form. 

 

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Scheduling 

  • Your committee should meet at least once per year for PhD students and every six months for CD 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 GG Coordinator can help with scheduling. You should first find a set of times that work for your advisor, and then work with the rest of the committee to find a mutually agreeable time. 
  • As soon as the meeting is scheduled, inform the GG 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 GG Coordinator at least one week prior to the meeting.

Presentation

  • Send your presentation to the GG Coordinator. It can be sent either before or after meeting.
  • The student is expected to lead the discussion during the thesis committee meeting. The thesis advisor is free to 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 coordinator if you need a copy of your previous eval

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 coordinator.
  • Please contact the coordinator with any questions regarding these forms.

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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 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.

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Scheduling your defense:

  • Review the graduation calendar dates.
  • Work with your advisor and committee members to find a mutual date/time.
  • Inform the GCB coordinator when your defense is scheduled, so she can help you reserve a room.

Before your thesis defense:

  • Register on-line for your degree at: https://fission.sas.upenn.edu/sso/gas/degree/app-start.php.
  • 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 talk can be announced and paperwork can be prepared. Feel free to also send a picture of yourself, or your research to be used on the talk advertisement flyer.
  • 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 Graduate Division office (215-898-7444, gas-degree@sas.upenn.edu). Do not wait to make an appointment, as they fill up fast. When your appointment is scheduled, inform the GCB coordinator of the date.
  • Email Anne-Cara in BGS your title page a few days before you defend. She'll check to make sure it's formatted correctly. After your title page is approved, have your advisor sign three copies of your title page. Bring these copies to your defense and give them to the GCB coordinator.

After your defense:

  • Pick up your signed title pages and form 153 from the GCB coordinator. You'll need to take these to your deposit appointment.
  • Fill out form 154 with post graduation information.

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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 his or her progress in the PhD program and status as a PhD or combined degree student. The IDP is due August 1 of each year for GCB students.

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.

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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

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

Please contact Maureen with any questions related to the above.

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