For 1st and 2nd years

PhD lab rotation schedule -
Lab Rotation 1, September 20 - December 3
Lab Rotation 2, January 3 - March 18
Lab Rotation 3, March 28 - June 3
*each rotation lasts 11 weeks

Combined Degree lab rotation schedule -
Lab Rotation 2, August 15 - October 14 (third year fall term)
Lab Rotation 3, October 17 - December 16 (third year fall term)
*rotations 2 and 3 are 9 weeks

Please keep in mind that the start and end dates for each rotation are somewhat flexible. Meaning you can start a week earlier/later than what is indicated above if it works better for the lab you are working in. You just need to be sure to complete the required 9 or 11 weeks. If you happen to work out a different schedule then what is listed above, just let Anne-Cara know.


What advice do you have for choosing a lab rotation?

  • Talk to senior grad students and ask for their advice
  • Choose a lab which would help you become a successful scientist (if you want to be one) or help you get a position in industry (if you want one).
  • Don't be afraid to choose outside of your area of "expertise." It will be a learning experience no matter what, and it's a great time to have fun going outside your comfort zone.
  • Don't feel like you have to choose related labs. Sometimes choosing distinct research topics can help you figure out what really excites you.
  • Start thinking about potential rotations early. Leave yourself enough time to talk to several different professors.
  • Don't be afraid to branch out into a research area you don't know much about -- rotations are one of the best times to try new things!
  • Meet with students currently in the lab, as well as students who have rotated through the lab but chosen not to join.
  • Choose someone who works on science you are interested in.
  • Beyond looking at faculty webpages/publications to find labs that might study topics that are interesting to you, go to events where you can hear faculty talk about their research (chalk talks, seminars, etc.) and also events where you can talk to faculty in a more casual setting. It's a good way to ensure you get along with your potential PI as well as ask about their research without a formal meeting.
  • Ask other students whom they rotated with and what they liked/didn't like about their rotation.
  • Try to work out a specific project that you can work on and what you might work on for your thesis work if you join the lab. You shouldn't worry about working out specific details, but the professor should have directions they're looking to explore in their research and they should be looking for students to own those projects.

What resources did you use to help in choosing your rotations?

  • Discussion with senior faculty.
  • Speak with senior grad students - they know generally what professors are working on, what the professors are like, and whether students in the lab are generally happy and successful.
  • talking to other students and listening to faculty talks at the beginning of the semester.
  • Faculty pages / lab websites.
  • GCB website.

Contact Anne-Cara for a list of students who have rotated in the lab(s) you are considering.


Candidacy Exams will take place in late May. The Candidacy Examination consists of 2 parts: a written Proposal describing plans for the thesis project, and an oral Defense of that document. 

Orientation | WorkshopsWritten Proposal Guidelines | Oral Proposal Defense | General Knowledge | Timeline | Role of Thesis Advisor | Uniform Examiners and Committee | Exam Procedure | Possible Outcomes


There will be a meeting in December to go over all the details for the Candidacy Exam. 


Four workshops are scheduled in February and March to help students prepare for their exams. Topics include: Overview of Scientific Writing, General Grant Writing, and Specific Aims review. 

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. Please visit here for further instructions.

Oral Proposal Defense

Structure of the Oral Exam

• Exams are scheduled for 120 minutes but often completed in ~90 minutes
• Prepare a 15 minute overview of proposal with no more than 15 slides
• 1 page handout can be given to committee with complex diagrams if needed
• You’ll be able to present for about 15 minutes without interruption
• You may use the white board in response to questions during the discussion to explain additional aspects not included in your slides

A simple guide to the Oral Exam

• Intro slide should include all two/three aims;
• 3-5 slides should illustrate the background and the significance of the question;
• 9-11 slides should cover your specific aims (the approaches proposed to address each aim).

General Knowledge
Students will also be evaluated on your general knowledge of genomics and computational biology. Topics to be familiar with are included in this document.


  • December: Orientation
  • Jan-March: Workshops
  • April 1: Submit the title and specific aims of your proposal to the Graduate Group Chair for approval and also provide a copy to the Graduate Group office. The specific aims should be no more than one page. The GCB chair will evaluate the specific aims and get back to the student with approval or suggestions for revisions. If the aims need to be revised, the student will return the revised aims until they are approved.
  • April 15: Final version of Aims due
  • Early May: You will be informed of the composition of your examination committees and date/time of the examination. Once faculty are chosen to sit on the examination committee, the student should not contact those faculty any longer.
  • One week before scheduled exam: Email a copy of your proposal to the Graduate Group office, the Graduate Group Chair, and each member of your committee. 
  • Late May: Examinations are administered.

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

Students are encouraged to consult with their Thesis Advisor(s) 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. The Thesis Advisor is excluded from being on the Preliminary Examination committee for their own student and has no role in determining the composition of the committee.

Uniform Examiners and Committee

The purpose of having a Uniform Examiner on the committee is to be able to compare all exams with respect to rigor and the decision making processes of the different exam committees. With this information, uniformity in decisions can be established. These examiners will be responsible for the evaluation forms that constitute the written record for the exam.

The remainder of the committee will be chosen by the GCB 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.

Exam Procedure

A Week before the Exam

As indicated in the timetable for preparation of the preliminary exam proposal, email each member of your committee a copy of your proposal the week before your exam.

On the Day of the Exam

A faculty member will serve as the Uniform Examiner of each committee. Examinations will be scheduled to allow 1.5-2 hours for each exam. When the committee has gathered and the members have been introduced to the student, the Uniform Examiner should ask the student to leave the room briefly. The topics to be discussed in the student's absence are:

  • The student's overall record. Any deficiencies that might need special attention in the oral questioning should be identified.
  • The quality of the written proposal. If the quality is so poor as to be unacceptable, the student can be given a "fail" at this point.
  • If the proposal is generally acceptable, any specific deficiencies revealed in the written proposal should be identified and pursued in the oral questioning.
  • The "ground rules" for the examination should be established. The student should prepare a 15 minute presentation. The committee members should plan to let the student give the presentation uninterrupted except for questions of clarification.

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. 

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 Uniform Examiner feels that the student has been examined sufficiently, they 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).

Possible outcomes


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, they will discuss the conditions of a conditional pass with the student involved.


This is the outcome when the written proposal, the oral defense, and/or grades from coursework are unacceptable. The GCB chair, in consultation with the prelim committee, the Uniform Examiner and the thesis advisor(s) will decide if the student should be given a chance to retake the oral exam. Students who are given this option must do so within the time frame decided by their prelim committee and GCB chair. If no remediation is granted, the student will be dismissed from GCB. In the case where dismissal is deemed necessary, the student may be eligible for a terminal Master’s degree if all other requirements have been met.




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.

GCB IDP schedule:

  • 1st years: Meet with your advisor(s) to complete/discuss your IDP before meeting with the advising committee in the summer before your 2nd year.
  • 2nd years and 3rd year CD students: Meet with your advisor(s) anytime to complete/discuss your IDP by the August 1st deadline.



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.


  • 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 including 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.


  1. GCB pods, which are composed of students from all years, are meant to help first-year students transition to Philadelphia and become acclimated to GCB. Each year, pods are formed in August.
  2. During the first year of the program, GCB students do not have a permanent lab and mainly rely on other students for guidance on courses, rotations, fellowship applications, etc. In addition to the cohort of students, select PIs (“accessory PIs”) volunteer to advise first-year students as they move through rotations and courses.
  3. Graduate school presents many challenges and students should not feel like they are going through these experiences alone. Each month, peer mentoring sessions are held for students to share their experiences in the program and voice any concerns they might be having related to EDI. These sessions are meant to be open times for students to chat about anything that is on their minds and get advice and support from their peers. Concerns raised by students will be funneled to the EDI committee in order to work on possible solutions.
  4. Panels for selecting courses and choosing rotation labs give first-year students a chance to hear about the experiences of upper-year students and how they chose to design their curriculum and what criteria they used when choosing labs to rotate in. See Student Advice for Choosing a Lab Rotation for more information on choosing rotation labs.