Genomics and Computational Biology

 

 

 

Graduate Group Handbook

 

July, 2016

 


Table of Contents

Training Mission

Policies for Faculty

Requirements for Graduate Group Membership

Faculty Participation

Governance of the Graduate Group

Administrative Structure of the Graduate Group

Chairperson

Vice Chair

Executive Committee

Curriculum Committee

Admissions Committee

Advising Committee

Mentoring GCB Students

Rotation Policies

Thesis Mentoring Policies

Role of Thesis Committee Members

Co-mentorship

Policies for Students

GCB Curriculum

General Requirements of the Doctoral Program

Course Requirements

Sample schedule under new system:

Lab Rotations (GCB 699)

Pre-dissertation Research (GCB 899)

Qualifying Approach and Biological Specialty Courses

Seminars

GCB Chalk Talks

Penn Bioinformatics Forum

The Candidacy Process

Qualifying Review

Oral Candidacy Exam

Guidelines for the Written Proposal

Oral Proposal Defense

Timetable for Submission of the Preliminary Exam Proposal

Role of Thesis Advisor

Composition and Duties of Examination Committee

The Prelim Committee Chair, or his/her Designate

Experts

Thesis Advisor

Exam Procedure

Prior to the Day of the Exam

On the Day of the Exam

Possible outcomes

Pass

Conditional Pass

Failure

Thesis Research and PhD Mentorship

Thesis Committee Meetings:

Individual Development Plan

Committee Composition

Scheduling

Meeting Materials

Meeting Agenda

Meeting Report

Thesis Defense

Permission to Write

Scheduling the Defense

Defense Process

Dissertation Deposit

Academic Standards

Satisfactory Progress

Incomplete Coursework

Medical Leave

Master’s Degree

Recertification Process

Misconduct

Grievances

Financial Resources Available to Students and Faculty

Training Grants

Individual Fellowships

Travel Awards


Training Mission

 

The Genomics and Computational Biology (GCB) Graduate Group identifies outstanding PhD candidates, recruits them to the University of Pennsylvania, and trains them to be productive scientists in both the academic and industry arenas. The overall mission of our training program is to provide students with mentorship and help them develop the skills they need to become independent and interdisciplinary research scientists in genome sciences and computational biology, ultimately leading to the production of accomplished biomedical scientists regardless of particular approaches. However, because our graduates also pursue careers other than research, completion of our training program will also effectively prepare students as leaders in non-academic careers and opportunities. Pursuant to this overall mission, GCB seeks to provide each trainee with a comprehensive understanding of the foundation of genomics and computational biology. Students will learn the importance of both theoretical and experimental approaches, and how to apply these approaches to contemporary problems in biomedical sciences. As a result, students will learn contemporary, but also historical views associated with the study of genomics and computational biology.

 

GCB accomplishes its training goals by:

a) providing trainees with a foundation of knowledge through coursework, seminars, journal clubs, and interactions with visiting scientists;

b) training students to evaluate the current literature and develop questions into scientifically testable hypotheses;

c) providing trainees with an intensive basic research experience.

 

 

Policies for Faculty

Requirements for Graduate Group Membership

Faculty membership in GCB will be approved by the Executive Committee based on (i) the applicant’s current curriculum vitae (CV), (ii) and letter of request from the candidate, or a nomination letter from a current GCB faculty member. Candidates for membership in the Graduate Group are asked to give a chalk talk prior to joining the group, to introduce themselves and their research to GCB students and faculty. To remain in GCB, faculty are expected to participate in the functioning and activities of the group in a substantive way.

Faculty Participation

GCB faculty participation is tracked by the Biological Graduate Studies (BGS) program and by the GCB Coordinator. Several different types of activities are considered when evaluating participation and a faculty member’s standing, including:

Mentoring a GCB student in a rotation or on their thesis project is not considered adequate in and of itself to maintain membership in GCB. After a three-year initial membership and every three years thereafter, faculty that are not deemed to be contributing will be invited to contribute (in some cases, to a specific activity) in order to retain their good standing. If they prefer not to contribute, they will be removed from the list of active GCB faculty, but are welcome to rejoin the program at a later date.

Governance of the Graduate Group

The Graduate Group is overseen by the Chair and the Executive Committee with additional Advising, Curriculum, Admissions, and Candidacy Exam (formerly Prelim Exam) Committees. The Admissions, Advising, and Curriculum Committees each have non-voting student members representing the students’ interests. Faculty members of GCB have the opportunity to voice opinions and suggest new initiatives at the annual GCB Faculty Meeting.

 

Administrative Structure of the Graduate Group

Chairperson

The Chairperson is the individual responsible for governance of GCB. The GCB Chair oversees all committees of the GCB and selects Course Directors for all courses. The Chair is responsible for convening meetings of the Executive Committee and sets the agenda. The Chair also sets the agenda and presides over annual Faculty Meetings. Beyond these, the Chair is also charged with:

 

The Chair serves a three-year renewable term. In the spring semester of the third year of a term, the Executive Committee requests nominations for the Chair and then contacts the nominees to determine if they would agree to serve. After the first three-year term, the Executive Committee may reappoint the chair though a committee vote, and a member of the committee should inform the faculty and students. Nominations must be senior level (Associate or Full Professor) individuals from the Standing Faculty of the University. The Chair must also have significant experience in training Ph.D. level students.

Vice Chair

The Vice Chair is selected by the Chair and approved by the Executive Committee. A primary responsibility of the Vice Chair is to fulfilling associated responsibilities of the Chair, if s/he is unable (travel, emergency, etc.). The Vice Chair also serves in a supporting role for the Chair, with the following additional responsibilities:

Executive Committee

The Executive Committee is responsible for:

The Executive Committee is also responsible for maintaining integration of the various Graduate Group programs and to review significant changes in policy, direction, or intent as recommended by GCB Committees or members, prior to final presentation to the membership at large. The committee functions as an advisory committee to the Chair on the following issues:

 

The Executive Committee is composed of the GCB Chair and other faculty selected from senior membership of the GCB, including members representing the concerns of the Advising, Curriculum, and Admissions Committees and other institutions that are traditionally heavily involved in GCB daily operations, as well as additional members appointed by the Chair to represent important aspects of student training. The Chair of the Executive Committee is the GCB Chair, who is responsible for leading meetings and setting the agenda.

 

Curriculum Committee

The Curriculum Committee is responsible for:

The Curriculum Committee is primarily composed of course co-directors for GCB courses (GCB 534, GCB 535, GCB 536, GCB 537, and GCB 752). The Chair of this committee prepares the agenda, runs the committee meeting, and sits on the GCB Executive Committee. The Chair of the committee, along with the Graduate Group Chair, attends BGS Curriculum Committee meetings. Modifications to the existing curriculum are initiated by this Committee and approved by the Executive Committee. Two GCB students serve on this Committee.

 

Admissions Committee

The Admissions Committee is responsible for:

 

The Chair of the Admissions Committee sits on the BGS Admissions Committee and represents GCB. They also serve as a member of the GCB Executive Committee, and work with the Graduate Group Coordinator to prepare admissions materials and reports for committee meetings. Three GCB students serve on this committee, and assist the Graduate Group Coordinator with planning activities, and other aspects of “hosting” the recruits.

 

Advising Committee

The Advising Committee is responsible for:

This committee consists of faculty members with diverse areas of expertise and from different departments/schools who meet with first and second year students at the beginning of each semester to advise and approve of each student’s course and rotation choices. These faculty members are expected to be familiar with their respective departments’ course offerings as they might apply to GCB students. Members of the Advising Committee also meet with first year students at the end of their second semester or in the summer prior to the second year to review the students’ progress, rotations, and plans for the coming year. Student members of the advising committee will offer their advice but not be privy to their colleagues’ transcripts or other formal evaluations. Student representation should include 2nd and 3rd year students to provide up-to-date feedback on courses.

 

Mentoring GCB Students

Hosting GCB thesis and rotation students is one of the privileges of GCB membership, because our students bring creative thinking and specialized skill sets to the lab. As such, students should not be treated as simply core bioinformaticians. Like any thesis lab, a PhD mentor must ensure that dissertations comprise independent, novel, demonstrable scientific advances, specifically along the axis of methodology and computational biology.

Rotation Policies

GCB requires 3 rotations, including at least one experimental project and one computational project. At the end of the rotation, the student is required to submit a one-page report on the rotation project, in NIH PHS 398 format. Grades are based on the student’s laboratory skills, accuracy, knowledge of relevant literature, self-motivation, perseverance, effort, and communication skills, and should be submitted to the Graduate Group Coordinator at the rotation’s end, along with any additional comments.

The student should use rotations to identify potential mentor(s) and labs that can support the student’s dissertation work. Rotation mentors are not required to have sufficient funds for the student to join the lab permanently, but in such cases the student should be informed before the rotation begins. If there is the potential for the student to join the lab permanently, the student and mentor should maintain communication about expectations and future plans.

Thesis Mentoring Policies

Students are expected to select a thesis mentor during the summer before their second year, and no later than the end of the third semester. Once a faculty member has agreed to mentor a student, the student requests approval from the GCB Chair, and BGS contacts the faculty member to determine funding sources for the student’s support. Mentor support begins June 1st of Year 2, after the 4th semester has ended and the Qualifying Exam is over.

Role of Thesis Committee Members

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.

Co-mentorship

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.

Policies for Students

GCB Curriculum

Training in Genomics and Computational Biology involves coursework, seminars, interactions with outside scientists, and research. These activities will impart a comprehensive knowledge of genomics and computational biology and teach the skills necessary for a career in biomedical science.

 

General Requirements of the Doctoral Program 

Students in GCB take courses as described below, do lab rotations with GCB faculty, and attend the research seminars sponsored by the Institute for Biomedical Informatics (IBI), the seminar series of their host department, as well as weekly student-faculty “chalk talks”.

 

The GCB curriculum combines several required courses specifically designed for the GCB program and additional courses available from other programs. In general, the core courses are taken during the first year, although this is not required. In the first year, students take three courses and participate in one lab rotation each semester. During the second year, the lab rotation is replaced by pre-dissertation research in the student’s thesis lab under the direction of their mentor.

 

In view of the highly varied academic backgrounds of students in GCB, members of the Advising Committee meet with each student individually once per semester (Year 1 and 2) and plan courses and rotations. Under the GCB curriculum, students are required to complete a minimum of ten classes, as specified below. The advising committee helps design a course schedule for each student that matches his/her needs and interests, aided in part by the completion and discussion of the NIH-required Individual Development Plan.

Course Requirements

GCB students will be required to take 7 “core” courses. The required courses are:

The remaining courses will consist of electives of the student’s choice for a total of 10 courses (6 for combined degree students). In Year 1, students will be expected to take 3 courses per semester (plus rotations). In Year 2 that number is reduced, and students will be expected to take 2 courses per semester (plus pre-dissertation research). They will receive 2 CUs per semester for their Pre-Dissertation research, and are expected to put more time into their lab work than they did as first year students.

Sample schedule under new system:

PhD

Fall

Spring

Summer

Year 1

GCB 534 (1 CU)

GCB 536 (1 CU)

Elective (1 CU)

Rotation 1 (1 CU)

GCB 537 (1 CU)

BIOM 555 (1 CU)

Elective (1 CU)

Rotation 2 (1 CU)

Rotation 3 (1 CU)

Pre-dissertation research (1 CU)

Year 2

Elective (1 CU)

Elective (1 CU)

Pre-dissertation research (2 CUs)

GCB 752 (1 CU)

Elective (1 CU)

Pre-dissertation research (2 CUs)

Qualifying review (mid-May)

Oral defense (late May)

Combined degree

Year 3 (Year 1 of PhD)

GCB 534 (1 CU)

GCB 536 (1 CU)

STAT or Approach Elective (1 CU)

Rotation 2 (1 CU)

GCB 537 (1 CU)

STAT or Approach Elective (1 CU)

Elective (1 CU)

Rotation 3 (1 CU)

Qualifying review (mid-May)

Oral defense (late May)

 

Lab Rotations (GCB 699)

Because it is essential that candidates have a firm training in biology and experimental techniques, a crucial component of the GCB curriculum is research rotations in the laboratories of GCB-affiliated faculty. Students in this program are required to do three lab rotations as part of their training. The definition of a lab rotation is flexible and includes the possibility of rotations in a computer science lab (for example, the application of data mining techniques to biological information sources) or a course of directed reading and research in mathematics/statistics, but students should expect to spend at least 25 hours per week in their rotation lab. At least one rotation must be a wet-lab project, and one must be computational.

 

Each rotation lasts 11 weeks, with the first rotation beginning towards the end of September, the second rotation beginning during the first week of January, and the third rotation beginning in late March and running until mid-June. Students submit a one-page report at the end of the rotation, and will be evaluated and graded by the supervising faculty member. The dissertation laboratory is usually chosen from one (or more) of these rotation labs, although this is not required. To ensure breadth of the training experience, all laboratory assignments must be approved in advance by the GCB Chair or the Chair of the Advising Committee.

Pre-dissertation Research (GCB 899)

Once the student has identified a thesis lab, generally during their first summer and no later than the end of their third semester, they begin graded lab work in their chosen dissertation laboratory. These lab projects serve as a foundation to the more formal dissertation research that follows the Candidacy Exam.

Qualifying Approach and Biological Specialty Courses

Approach Courses

Biological Specialty Courses

BSTA 621: Statistical Inference I (Spring)

BIOL 410: Advanced Evolution (Fall of odd years)

BSTA 630: Statistical Methods and Data Analysis (Fall)

BIOL 483: Epigenetics (Fall)

CIS 502: Algorithms (Fall)

BIOL 485: RNA World (Spring)

CIS 519: Intro to Machine Learning (Fall)

BIOL 493: Epigenetics of Human Health (Spring)

CIS 520: Machine Learning (Fall)

CAMB 431: Genome Science and Genome Medicine (Spring)

CIS 550: Databases (Fall)

CAMB 532: Human Physiology (Fall)

CIT 590: Programming Languages and Techniques (Fall)

CAMB 550: Genetic Principles (Spring)

This list is not exhaustive, and additional qualifying courses may be approved by the Advising Committee and GCB Chair.

Seminars

Students are required to attend the monthly Penn Bioinformatics Forum (PBF) seminar series, departmental seminars, and GCB Chalk Talks. The Graduate Group tracks attendance and participation in these activities, and they are considered an integral part of the GCB curriculum.

GCB Chalk Talks

Chalk Talks offer students an opportunity to present their research to other GCB students and faculty. In these talks, students are paired with a faculty member, with each giving a half-hour talk. GCB Chalk Talks also provide the opportunity for GCB faculty candidates to present their research, and for students to learn more about potential lab rotations.

 

Penn Bioinformatics Forum

The Penn Bioinformatics Forum has a long history of bringing top speakers in bioinformatics from academia and industry. All GCB students are invited for a lunch meeting with the PBF speakers. GCB students and students also organize two PBF seminars per year (i.e. they select speakers, send the invitations, organize the schedule and meet with speakers on an individual basis, while Penn faculty meet the speaker for lunch and dinner as a group).

 

The Candidacy Process

Qualifying Review

Students will be evaluated on their performance in the required “core” courses, plus their chosen “Approach” and “Biological Specialty” electives. GCB will compile a list of “qualifying” courses (see above), and any substitutions will need approval from the Advising Committee and the Graduate Group Chair. The combined GPA for these 7 courses (6 for combined degree students and those who place out of GCB 536) must be a 3.5 or above, with no grade lower than a B.

If a student earns a B- or lower in any of the Qualifying Review courses prior to the fourth semester, they may retake the course, and the second grade will count toward the review. In some cases, the Advising Committee may recommend a substitute course instead of a retake.

The Advising Committee will be responsible for conducting the review and informing the Graduate Group Chair. This process should be completed before the student’s Oral Defense is allowed to take place.

 

Oral Candidacy Exam

The Candidacy Examination consists of 2 parts: a written Proposal describing plans for the thesis project, and an oral Defense of that document. If there is not a well-developed thesis project by winter of the prelim exam year, the proposal can be focused around any problem central to the work in the thesis lab.

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.

There is no expectation that extensive preliminary data should exist, but if it does, present it within the Research Strategy section (remaining within the 6 page limit). For example, such data might be included as part of the rationale or justification for a particular approach. Any preliminary work that represents unpublished data of others from the thesis lab should be explicitly approved by those providing such data and be properly cited.

The emphasis of the proposal should not be on a review of the literature but on dealing creatively with the problem selected. The proposal should be "hypothesis-driven". That is, it should aim explicitly to address a working hypothesis regarding an unresolved issue in Genomics and Computational Biology. It is important to remember that the proposal should describe work that can reasonably be done by one person in 3-4 years, not what an entire lab of people could accomplish in 3-4 years. In this respect, the written Proposal will be more focused than a mentor’s NIH R01 application. This proposal is only a starting point for the actual thesis work. The approaches and experiments can reasonably be expected to change over time with input from the Thesis Advisor and the Thesis Committee.

Oral Proposal Defense

For the Proposal Defense, there is an expectation of substantial depth of knowledge in the thesis area, broadly defined. Thus, it will not be sufficient to defend only the particulars of the proposed experiments. A key element of the oral examination will be to explain and defend the importance of the questions to be addressed, and to place these questions in the broader context of the field. Thus, in both the Significance section of the written Proposal and in the subsequent oral Defense, the student should be able to marshal knowledge from the relevant literature and from broader areas of Genomics and Computational Biology. Each student's performance will be evaluated on: 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 (covered in coursework).

Timetable for Submission of the Preliminary Exam Proposal

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

The student is encouraged to consult with their Thesis Advisor 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. It is the Thesis Advisor's responsibility to ensure that the overall objectives of the proposal are worthwhile. The student can discuss potential experimental approaches with his/her advisor or others.

Composition and Duties of Examination Committee

The Prelim Committee Chair, or his/her Designate

Ideally, the Prelim chair should be present at all exams. The purpose of the Prelim Chair’s presence on the committee is to be able to compare all the exams with respect to rigor and the decision making processes of the different exam committees. With this information, uniformity in decisions can be established. The final decision for each exam (pass or fail) will be made by the Prelim Chair, and then made known to the student by the Graduate Group Chair after all exams are completed. In making these final decisions, the Prelim Chair, will consider the committee's recommendations along with the comparative rigor of all the exams. The Prelim Chair will be responsible for the evaluation forms that constitute the written record for the exam.

Experts

The remainder of the committee will be chosen by the Prelim 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. They should be selected to provide a balance between junior and senior faculty.

Thesis Advisor

The Thesis Advisor is explicitly excluded from being on the Preliminary Examination committee for their own student and has no role in determining the composition of the committee.

Exam Procedure

Prior to the Day of the Exam

As indicated in the timetable for preparation of the preliminary exam proposal, each student will provide each member of his/her committee with a copy of the proposal. In addition, the GCB office will provide a copy of the student's file to each examiner. Faculty should read and review both of these documents prior to the exam. Any problems with the submitted proposal should be held for discussion at the committee meeting.

On the Day of the Exam

The Prelim Chair will serve as the chair of each examining committee or should ask one of the other members to take on this role. Examinations will be scheduled to allow 1.5 hours for each exam. When the committee has gathered and the members have been introduced to the student, the chair should ask the student to leave the room briefly. The topics to be discussed in the student's absence are:

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. If questioning is slow in getting started, the committee chair should lead off by asking a question. The chair should then turn over the questioning to one of the other examiners. In a rotating fashion the other examiners should question the student.

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 chair feels that the student has been examined sufficiently, he/she 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). Additional comments can also be added. These should include an assessment of the student's perceived strengths and weaknesses. These signed forms are returned to the Prelim Chair at the end of the exam. They become part of the student's file. The student will be informed that the outcome of the exams will be made known at the end of the exams for the program. In most cases this is within a few days.

Possible outcomes

Pass

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, he/she will discuss the conditions of a conditional pass with the student involved.

Failure

This is the outcome when either the written proposal or the performance on multiple aspects of the exam are completely unacceptable. If the overall performance of the student was weak, or if there were significant deficiencies in more than one of the areas being evaluated, the student will fail the exam. Students who fail the Candidacy Exam will be told why in the most specific terms possible. A student who fails will get a chance to rewrite the proposal and defend it at another oral examination.The possible outcomes for the second exam are Pass or Fail. A student who fails the exam twice must leave the program and has the option of obtaining a Terminal Master's Degree.

 

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 Meetings:

Once a student enters their Candidacy phase, they must meet with their Thesis Committee at least once per year. The purpose of the Thesis 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.

Individual Development Plan

The student and mentor should meet in the two weeks prior to the annual thesis meeting to discuss and complete the NIH-mandated Individual Development Plan. The second page of the plan, which becomes part of the student’s record, should be discussed with the Thesis Committee and subsequently submitted to the GCB office.

 

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. The chair must be of Associate Professor rank or higher, and must be a member of GCB. The chair should also not have any close ongoing collaborations with the student’s advisor. 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 Graduate Group Coordinator, who will provide the necessary forms to the committee chair.

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.

Thesis Defense

Permission to Write

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 must be convened and permission must be reissued. 

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. The student must submit the title and abstract to the Graduate Group Coordinator at least one month before the defense date, so that the public talk can be announced. 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. Thus, before the final draft is submitted, each committee member can identify necessary revisions and suggest improvements.

Defense Process

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 a certification form, which is then submitted to the GCB Chair for signature. 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.

Dissertation Deposit

After the thesis is approved by the Thesis Committee, the student must schedule an appointment to deposit the dissertation with the Graduate Division office. The Graduate Division will follow up with information about specific paperwork. The Dissertation Manual, including templates, and online application for graduation can be found on the Provost’s Dissertation Resources page. The final electronic version is submitted online the day before the deposit appointment, and final hardcopy, signed by the student’s advisor and the Graduate Group Chair, is given to the Graduate Division during the deposit appointment.

 

Academic Standards

Satisfactory Progress

In conjunction with the Biomedical Graduate Studies Curriculum and Academic Standards Committee, the GCB Advising Committee is responsible for tracking students’ progress throughout the course of their studies. This includes coursework, lab rotations, and thesis-level progress. In order to remain in the program, students must maintain at least a B average (3.0 cumulative GPA) and make adequate progress in their research (as determined by rotation/thesis advisor and thesis committee, if applicable). Any student receiving a grade lower than a B- minus is put on academic probation and required to retake the course or a substitute designated by the Advising Committee.

 

Incomplete Coursework

Under exceptional circumstances, students who are unable to complete the work assigned in a course may request that the instructor issue a temporary grade of Incomplete (I). The student should then work with the instructor to put together a timeframe for making up the missed work. The maximum time allowed by the university is one year. Whether or not an incomplete grade is acceptable in a given situation, and the length of time allotted to make work up, are at the instructor’s discretion.

 

Medical Leave

Students are expected to attend class and be present in the lab. Many courses include attendance and participation as a key component of the final grade, and instructors/advisors are permitted to request documentation for any absence. Extended absences (more than three consecutive days) require documentation from a health care provider certifying the medical necessity for the absence and the expected date of return to work, which can be subject to verification by the Graduate Group. Students who need to take a prolonged period of time off should apply for medical leave according to BGS procedures.

 

Master’s Degree

Students who leave the PhD program after the Candidacy Exam but before their PhD research is complete may receive a Master’s Degree if they complete sufficient original research and/or write a thesis of approximately 20 pages. The thesis work is overseen by the student’s mentor, and if the final paper receives approval from a two-member committee (one member of the GCB Executive Committee and one other faculty member), the Graduate Group Chair will request a Master’s Degree be awarded by the Biomedical Graduate Studies Program.

Recertification Process

For students who reach a fifth year post candidacy, several steps will be taken to establish the underlying basis for inordinately slow academic progress, and to reach agreement on how to proceed to best serve the student. This process will occur annually, if need be, for students beyond their 5th year post candidacy. The student, his/her mentor, and the thesis committee chairperson will meet with an ad hoc subset of the GCB Executive Committee and will review all work completed to date, outline any extenuating circumstances that may have delayed progress, and propose an academic plan and timetable for completion of the degree, not to exceed one year. Exceptions to this rule may be considered by the Executive Committee only under extenuating circumstances, (e.g., a student has changed thesis laboratory during their training, but is making satisfactory progress in the new lab). Following this presentation and any discussion, and in the absence of the mentor and student, the ad hoc committee will confer and will EITHER: (1) Recommend extension, indicating their rationale for deciding that satisfactory academic progress is being made. They may accept the plan for completion of degree as submitted or further modify to the plan, at their discretion. The plan will be conveyed in writing under the GCB Chair’s signature to the student, mentor, and thesis committee chair. In addition, the GCB Chair, or a designee, will become an ex officio member of the thesis committee. The student and mentor will then meet with the thesis committee and report milestones at four month or more frequent intervals, with the Chair acting as liaison to the executive committee; or (2) recommend a terminal masters degree, with an outline of requisites for conferral; or (3) recommend termination without degree. Upon satisfactory re-certification, the student must complete all requirements for the PhD, including deposit of the dissertation, within one year.

Misconduct

Please refer to BGS policies on academic and research misconduct.

Grievances

In the rare cases where a student has a grievance that cannot be resolved by speaking with their instructor/mentor, the student should request a meeting with the Chair and/or Vice Chair. Each case is handled individually, involving GCB governing committees and faculty as needed.

Financial Resources Available to Students and Faculty

BGS students are funded for their first two years by the BGS program. Starting in June after the student’s 4th semester, funding becomes the mentor’s responsibility. Students can apply for supplemental fellowships or grants to reduce the burden on their mentors.

 

Training Grants

In addition to support from faculty mentors’ labs, GCB students may also receive financial support for tuition and stipend from one of Penn’s NIH training grants. 

Individual Fellowships

In addition to NIH training grants, students may apply for individual fellowships from a variety of organizations. GCB students have been supported by the following fellowship sources: Penn Genome Frontiers Institute, United States Department of Energy, NSF, NIH, and the United States Army.

Travel Awards

Thesis phase students are encouraged to attend academic conferences related to their thesis, and additional funds are available beyond what the mentor is able to provide. Students are eligible to receive travel awards from BGS and the Graduate and Professional Student Association for one conference per year, but may receive mentor support to travel to additional conferences as deemed appropriate.