Handbook
PREAMBLE
The Biochemistry Biophysics and Chemical Biology (BBCB) graduate program is designed to prepare students
for careers as independent investigators, educators scholars and leaders in the area of modern
biochemistry and molecular biophysics, and more broadly in biomedical science. BBCB follows the policies and procedures
of the University of Pennsylvania, and
Biomedical Graduate Studies (BGS) the umbrella organization that provides
administrative and logistical support to the seven graduate programs centered in the
Perelman School of Medicine at the University of Pennsylvania.
In addition BBCB follows the Graduate group specific procedures and policies described in this document.
ADMISSION
Admission for Ph.D. study is offered to students with good undergraduate training in biochemistry, physics,
organic chemistry, physical chemistry, biology, and mathematics.
The BBCB program especially encourages applications from minority students and students with disabilities.
Students lacking preparation in a
particular field, but otherwise qualified, may be admitted and given the opportunity to strengthen
their backgrounds by taking the appropriate courses. The Graduate Record Examination (GRE) General Test is not
required; The Admissions Committee screens completed applications and decisions on admissions are based on
undergraduate record, including research experience, letters of recommendation, and personal interviews.
TOEFL scores are required for foreign students whose native language is not English.
Admission decisions are usually completed by late March.
Application to BBCB is done through Bomedical
Graduate Studies' centralized
Ph.D Admissions Portal
Students accepted for admission into the Ph.D. program receive tuition, and health care and insurance reimbursement, plus a twelve-month competitive stipend. Awards are renewed annually for students in good academic standing. Support for graduate students comes from a variety of sources, including Biomedical Graduate Studies, training grants, faculty research grants, and from private foundations such as the Howard Hughes Medical Institute. Applicants are urged to apply for scholarships from the National Science Foundation and other funding programs for graduate students. A limited number of fellowships are available for outstanding foreign students.
PROGRAM REQUIREMENTS
The program comprises the following didactic and training elements: Laboratory Rotations, Formal Courses
(lecture based and seminar based), Responsible Conduct in Research, Scientific Rigor and Reproducibility,
Oral and Written Scientific Communication skills, all revolving around Immersive Training in Research.
Modern scientific research is a highly collaborative activity, and students
are expected to forge appropriate collaborative interactions within and between labs to best forward their
own dissertation research. In addition
students are expected to fully partake in the scientific community as Penn, including
attending appropriate research seminars and participating in the annual retreat.
There are also various working groups that focus on research sub-specialties
and other BBCB activities
Specific Course Requirements evolve with the progress of science, and are described in the
BBCB Curriculum Document
Forms and various paperwork required during the program are maintained on a
separate web page
Forms and Templates
ACADEMIC ADVISING and beyond
Course advising is the responsibility of the Advising Committee. In view of the variety of backgrounds
of the students in the program,
the Committee reviews the background of each student, and in consultation with the student,
decides on his or her curriculum. The goal is to provide a flexible yet structured program so
students of different backgrounds will receive the appropriate training for their research interests.
Each incoming student meets individually with the Advising Committee during orientation week to select their fall courses,
and at the end of December to select spring courses. Advising is held in early May to discuss summer lab rotations.
Rising second year students meet individually with the Advising Committee mid-July to discuss fall courses
and at the end of December to select spring courses, although some students may not need this second meeting
if they have fulfilled all course requirements.
Students are assigned a student mentor as soon as they are accepted into the program. The role of the mentor is
to provide informal advice on more general aspects of graduate education, such as adjustment to graduate life,
guidance in career paths, and to advise a student in choosing a Thesis Advisor.
In addition to the regular advising provided by the Advising Committee, the BBCB Graduate Group and its
umbrella organization, Biomedical Graduate Studies provides support
and training for other practical issues of being a Ph.D student. These include topics such as scientific writing, applying
for fellowships, how to get the most out of your thesis committee.
Career Services provides a wealth of career
information on its website. It works with all Penn students to help them define career goals through individual
counseling and workshops on a wide range of topics from resume writing to interview to networking. It also sponsors
on-campus recruiting sessions and maintains lists of job opportunities.
The University of Pennsylvania is committed to the health, safety and well being of all its students. A centralized
Wellness Portal provides comprehensive information
if you need help in any non-academic area.
CANDIDACY EXAM
All graduate students affiliated with BGS (Biomedical Graduate Studies) are required to pass a Candidacy Examination
in the spring of the second year. In BBCB, this examination consists of both a written research proposal (in the
style of an NIH fellowship application) and an oral defense of the proposal. Only students in good academic
standing are eligible to take the Candidacy Examination. Detail of the format and requirements of this exam
can be found on the BBCB curriculum page
DISSERTATION STATUS
A. Composition of Thesis Committees
Working Thesis Committee
After passing the Candidacy Exam, the student must form a Working Thesis Committee and fill
out the "Working Thesis CommitteeApproval Form." The Working
Thesis Committee will be comprised of three faculty members; at least two must be members of the BBCB Graduate Group.
The Chair of the Working Thesis Committee must be a member of the BBCB Graduate Group. The thesis advisor is not a
member of the committee, but is expected to attend committee meetings.
Final Thesis Committee
The Final Thesis Committee includes all members of the Working Thesis Committee plus one external examiner.
The External Examiner is someone from outside the BBCB Graduate Group who is brought in as an additional examiner
for the thesis defense. The external examiner may be a member of another graduate group in BGS, a standing faculty
member at U. Penn, or from outside the university. The BBCB graduate group chair must approve the choice of external
examiner in writing. If it is not possible for the External Examiner to attend the oral defense, he or she will
be asked to provide a written report to the Chair of the student's thesis committee prior to the defense.
The Working and Final Thesis Committees should be constituted to include breadth as well as expertise in the particular research area of thesis work. The student and his or her advisor shall jointly select the members of the thesis committees. The student should submit in writing a list of potential committee members, indicating which faculty will serve as Committee Chair, to his or her Thesis Advisor and the Graduate Group Chair. The Graduate Group Chair will respond in writing to approve the composition of the Committee, or make recommendations for other candidates. The Graduate Group Chair will adjudicate any disagreement on the composition of the thesis committee. The student must register the composition of his or her thesis committees with the Graduate Group Office after approval by the Graduate Group Chair. Once the student obtains approval, they must fill out the Final Thesis Committee Approval Form.
B. Evaluation of Student's Progress
The Working Thesis Committee meets to monitor the students' progress every 6 months. A one-page summary of
progress and plans should be prepared by the student and submitted to the committee at least 2 days prior to the
meeting. The Working Thesis Committee will meet with the student in the absence of the
Thesis Advisor and vice versa . A written report will be prepared after
each meeting by the Thesis Committee Chair and will be placed in the student's academic file.
If the Committee and/or the Thesis Advisor are not satisfied with the student's productivity, the written report prepared by the Committee will outline a course of action. A copy of the report will be forwarded to the Graduate Group Chair, the student and the Thesis Advisor. The student will have the opportunity to reply to the written report of the Committee. Within 6 months, an additional meeting of the Thesis Committee will take place to determine the progress. If sufficient progress is not apparent by the next Committee meeting, the student will be asked to petition for a terminal Master's degree.
C. Preparation of Dissertation
The Working Thesis Committee will give written approval for the student to schedule the defense, but this does
not automatically mean that experimental work is completed. The student should be prepared to continue experiments
while writing and to rewrite or do additional experiments after the thesis defense if deemed necessary by the
committee. If the student has not already done so, at this point he or she should, in conjunction with the Thesis Advisor,
select the external examiner to form the Final Thesis Committee. The Graduate School of Arts and
Sciences (GAS) requires a dissertation to represent a definite contribution to scientific knowledge and to show that a
student possesses 'power of independent research.' The Graduate Group requires that the dissertation contain
original work that answers a well formulated scientific question or questions and that the dissertation display a
logical progression of scientific thought. It is expected, although not required, that this caliber of work will result
in one or more peer reviewed scientific publications with the student as a first or lead author, either already
published or under review by the time of the defense. Note that publication of a paper with the student as an author
does not automatically indicate sufficient quality and quantity of work to constitute a defensible thesis.
A written draft of the thesis is to be given to the examination committee at least two weeks prior to the defense,
and no later than six months from the date of permission to defend. Students are expected to work full-time
on the completion of the written draft of the thesis, and upon request demonstrate reasonable progress
to their thesis advisor and committee. If the student will not meet the six-month deadline for submitting the thesis,
they must meet with the committee
again before the end of the six months. The committee will review the student’s progress and set a new
deadline for the submission of the thesis. Under normal circumstances, no more than one additional month will be granted.
If the student does not submit the thesis or meet with the committee during the six-month period,
the graduate group will put the student on academic probation. The graduate group’s academic review committee
will determine whether the student should be given permission to defend the thesis, and under what circumstances,
or whether the student should be withdrawn from the graduate group or offered a terminal masters degree.
D. Thesis Defense
The thesis defense will take the form of a public lecture. The private portion of the defense will be conducted
solely by members of the Thesis Committee, and in the absence of the Thesis Advisor. The
decision on approval of the thesis will be made solely by a consensus of the Thesis Committee in the absence of the
student and the Thesis Advisor.
If a Thesis Committee member cannot attend the Defense, the student must meet with the Chair of the Graduate Group to discuss the circumstances and decide on a course of action. One possible outcome is that the missing Committee member must review the student's written dissertation and submit a critique to the chair of the Committee before the thesis defense, so that those comments and any questions can be included during the private portion of the defense and addressed in any revisions that may be made to the dissertation.
Students who are defending their theses must inform the Graduate Group Office at least two weeks in advance of the defense date, and supply the title of the thesis and place and time of the defense, as well as an abstract and a figure for the monitors announcing the defense. The Graduate Group Office will announce the thesis defense to the University community. The Graduate Group Office is responsible for completing the forms indicating that the thesis has been successfully defended. Before a student makes the appointment to deposit the thesis, he or she must provide the Graduate Group Office with a copy of the abstract page, a signed copy of the title page, and postdoctoral appointment information, if available.
Students should consult the Graduation Checklist as soon the Thesis Committee formally grants permission to schedule the defense.
OTHER PROGRAM INFORMATION
Academic Standards
The University standard for satisfactory academic progress is a 3.0 grade point average (B).
The minimum standard for final course grades in the BBCB Graduate Group is a B.
BBCB students who do not achieve the minimum grade for courses will be referred to the Biomedical
Graduate Studies Academic Standards Committee. The Academic Standards Committee will, in concert
with the BBCB Academic Review Committee's recommendations, impose sanctions such as academic probation.
In addition, the Academic Review Committee may ask a student to retake a course, continue course work
towards the terminal Master's Degree, or withdraw from the program. The Academic Review Committee
will review each case on an individual basis.
Training in Responsible Conduct in Research (RCR) and Scientific Rigor and Reproducibility (SRR)
This training is occurs from matriculation to graduation. It has several components: including lectures,web-based
training, program literature, small group discussion workshops and themed laboratory meetings.
Participation in all phases of the training
program is mandatory for all graduate students in the Biomedical Graduate Studies programs. The training program
begins with a faculty-led presentation to incoming students at the BGS new student orientation, which provides
an overview of responsible conduct of research and appropriate behavior in the classroom and lab. New students
are also given a copy of the Cold Spring Harbor publication, At the Bench(Kathy Barker, author) which
covers some aspects of RCR. See the BGS
RCR/SRR
website for further information.
Individual Development Plan (IDP)
Biomedical Graduate Studies has implemented a required an annual Individual Development
Plan (IDP) for all predoctoral students, the goals of which are to make sure students and mentors are
communicating openly and that students are working proactively toward developing the skills they will need to
succeed. All BBCB students will be meeting with either the Advising Committee (first and second year students)
or their mentors (dissertation students) once a year to discuss their achievements in the past year and their
plans for the following year. Guidelines and forms for the IDP can be found
here.
Transfer of Credits
Students who enter the program having taken similar courses at the graduate level at other institutions with a B
grade or better, may petition the Graduate Group for transfer of credits. The decision to approve transfer of credits
will be made in writing by the Graduate Group Chair. Up to eight courses may be transferred. Students who have taken
graduate courses at Penn through the College of General Studies (CGS) may apply to transfer up to four course units
toward the Ph.D. degree. Combined degree students may transfer as many as 14 course units from another Penn professional
or graduate program, but are required to take 8 course units of Ph.D. lecture courses and seminars. It is recommended
that incoming students review any courses that may be transferable at their meetings with the
Advising Committee in September.
Transfer from Other Programs
University of Pennsylvania students who are currently enrolled in another graduate group within BGS may be
considered for transferring into the BBCB Graduate Group. Students should express their interest in joining
the BBCB Graduate Group by writing a letter of intent to the Graduate Group Chair. The student will then meet
with the Chair to review his or her academic record and establish a plan for meeting the BBCB requirements.
Students who wish to transfer from graduate groups outside of BGS need to follow the same procedures as
regular applicants to the program.
Terminal Master's Degree
The BBCB Graduate Group does not offer study towards a Master's degree. However, the Graduate Group may award a
terminal Master's degree to students who choose not to continue in the Ph.D. program. In certain instances, the
Graduate Group Chair may recommend that students who have not performed satisfactorily in course work, the
Candidacy Examination, or dissertation research leave the program with a terminal Master's degree. The
University requires a minimum of 8 course units for the terminal Master's degree. A final paper may also be
required, as determined by the Graduate Group Chair and Academic Review Committee.
Leave of Absence
The University allows graduate students to take a leave of absence with the permission of the Graduate Group
Chair and the Graduate Dean. Information, requirements, and the procedure to initiate a leave of absence can be found
on the BGS wellness website
.
Family Leave and Time Off for Childbirth or Adoption
BBCB abides by the University’s policies for Family Leave and Time Off for Childbirth or Adoption.
The University policies can be found
here.
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