Graduate Group in Epidemiology & Biostatistics

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GGEB Faculty-Student Handbook 2015 - 2016

2015-2016 GGEB Facuty-Student Handbook (PDF)

2014-2015 GGEB Faculty-Student Handbook (PDF)

 

Graduate Group in Epidemiology and Biostatistics (GGEB)

Graduate Training Programs in
Biostatistics

Graduate Training Programs in
Epidemiology

Introduction

Overview

Application and Admission

Financial Obligations and Support

Resources for Students

Academic Policies

Elements common to MS and PhD Programs

 Masters of Science (MS) in Biostatistics

Doctor of Philosophy (PhD) in Biostatistics

Evaluation and Examinations

Teaching Assistants

Other Policies

Committees

 Academic Advisor

Course Requirements

Doctoral Seminar

Consulting Projects

Course Plans

PhD Examinations

Preparing the Dissertation

Non-credit Reqntsuireme

General Program Policies

Facilities

1. Introduction

This handbook serves as a reference manual for the graduate programs in biostatistics and the doctoral program in epidemiology at the University of Pennsylvania. It covers the graduate experience, from admission through required course work, examinations, and the MS thesis (biostatistics), and PhD dissertation in both programs. This is a living document; please bring errors and omissions to the attention of the Chair or Vice-Chair of the Graduate Group in Epidemiology and Biostatistics, or to the Chairs of the respective programs.

Many people made essential contributions to this handbook, most prominently Drs. Harold Feldman (Chair of the Department of Biostatistics & Epidemiology); Stephen Kimmel (Director, Clinical Epidemiology Unit); J. Richard Landis (Director, Biostatistics Unit); Ebbing Lautenbach, John Farrar, and Theoklis Zaoutis (members of the GGEB Epidemiology Educational Programs Committee); Daniel Heitjan and Phyllis Gimotty (the first Directors of Graduate Studies in Biostatistics); Kathleen Propert and Scarlett Bellamy; Marissa Fox and Catherine Vallejo (coordinators of the biostatistics programs) and Jennifer Kuklinski and Gabrielle Ostapovich (coordinators of the epidemiology program), as well as Thomas Kelly and Ann Facciolo (former administrators of graduate programs in the graduate group). 

Many others contributed in ways large and small, not least the students in the doctoral program, whose many relevant questions and experiences have led us to review our policies, consider their implications, and write them down clearly. We thank them especially and wish them the best in all their endeavors, at Penn and beyond.

John H. Holmes, PhD
Professor of Medical Informatics in Epidemiology at HUP, Department of Biostatistics & Epidemiology
Chair, Graduate Group in Epidemiology and Biostatistics
Chair, Doctoral Program in Epidemiology

Mary E. Putt, ScD, PhD
Professor of Biostatistics, Department of Biostatistics & Epidemiology
Vice-Chair, Graduate Group in Epidemiology & Biostatistics
Program Chair, Educational Programs in Biostatistics

Hongzhe Li, PhD
Professor of Biostatistics, Department of Biostatistics & Epidemiology
Chair, Graduate Program in Biostatistics

Marcella Devoto, PhD
Professor of Pediatrics and Epidemiology, Department of Biostatistics & Epidemiology and Department of Pediatrics
Associate Chair, Doctoral Program in Epidemiology
Chair, Graduate Student Admissions Committee, Epidemiology

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2. Graduate Group in Epidemiology and Biostatistics

2.1 Overview

The Graduate Group in Epidemiology and Biostatistics (GGEB) is responsible for developing and administering the PhD degree programs in epidemiology and biostatistics as well as the MS program in biostatistics. The PhD programs train individuals to be rigorous and independent academic investigators, able to apply and extend the range of approaches available in epidemiology and biostatistics to address questions in biomedical research. The objective of the MS program in biostatistics is to train individuals in the basic theory and applications of statistical methods, especially as applied to problems in the health sciences.

The GGEB is a member of the Biomedical Graduate Studies Program (BGS) in the Perelman School of Medicine of the University of Pennsylvania. It is comprised of faculty from across the university with interests in biostatistics and epidemiology. Notably, many of the members of the Graduate Group have academic appointments within the Department of Biostatistics and Epidemiology (DBE). The Office of Biomedical Graduate Studies provides oversight and coordination for the GGEB and six other graduate groups offering PhD degrees in the biomedical sciences.

Biomedical Graduate Studies (BGS) was established in 1985 and serves as the academic home within the University of Pennsylvania for roughly 700 students pursuing a PhD in the basic biomedical sciences. Although BGS is housed within the School of Medicine, it is composed of more than 600 faculty members across seven Penn schools and several associated institutes. BGS provides training and administration through seven graduate groups, some of which have distinct sub-specialty areas. Each graduate group has its own training mission, leadership, and staff, but there is often significant overlap among the groups in respect to faculty membership, courses offered, policies, and procedures. BGS provides centralized support to the graduate groups for admissions, student fellowships, curricular oversight, record-keeping, and other operations.

Additional, up-to-date information about BGS is available at http://www.med.upenn.edu/bgs/.

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3 Application and Admission

3.1 Affirmative Action

The GGEB values diversity and seeks talented students from all backgrounds. The GGEB does not discriminate on the basis of color, sex, sexual orientation, religion, national or ethnic origin, age, disability, or status as a disabled or Vietnam Era veteran in the administration of its educational policies, programs or activities, admissions policies and procedures, and scholarship programs.  Women and minorities are especially encouraged to apply to the GGEB's educational programs.

3.2 The Application Process: All GGEB Programs

Applicants must complete the standard BGS application form and submit three letters of recommendation. The application and letters should identify personal attributes, experiences, accomplishments, and goals relevant to success in graduate study in biostatistics or epidemiology, depending on the program.  Applicants who are currently enrolled in a degree program must arrange for at least one letter of recommendation to be sent from a faculty member in that program. Only original letters of recommendation written on official university or business stationery will be accepted. Official transcripts from all undergraduate, graduate, and professional schools are also required.  The transcripts must come directly from the institutions and must be originals.

3.2.1 Waiver of Fees for the Application

U.S. citizens and permanent residents may request a waiver in cases of documented financial hardship. To request a waiver, email the admissions coordinator for BGS prior to submitting your application (currently Aislinn Wallace: aislinnw@mail.med.upenn.edu). Explain your situation and reasons for requesting a waiver of fees. The coordinator may ask for additional documentation e.g. documentation by the Financial Aid Officer from a relevant undergraduate institution, or, if not applicable, documentation of information about income, assets, family situation, etc. University rules prevent the waiver of application fee for international applicants.

3.2.2 Graduate Record Examination (GRE)

Unless noted below, all applicants must provide an official score from the Educational Testing Service (ETS) for the Graduate Record Examination (GRE) General Test.  We do not require the GRE subject test.  GRE scores are valid for five years from the date taken. Students who are currently enrolled in the Biostatistics MS program and who are applying for admission to the Biostatistics or Epidemiology PhD programs but do not have a currently valid GRE may request a waiver of the GRE requirement.  Our ETS institution code is 2900.  Please do not enter a separate department code.

3.2.3 Test of English as a Foreign Language (TOEFL)

All applicants whose native language is not English must arrange for ETS to submit an official TOEFL score as part of the application by the application deadline. The TOEFL requirement is waived for a student who has been enrolled in an English-speaking university for at least two years upon application. TOEFL scores are valid for two years.

3.2.4 Application Deadline and Notification

Students are admitted once per year, for the fall term.  Information and application materials are available by October of the preceding year with an application deadline of around December 1. After reviewing the files, the Admissions Committees for the individual programs recommend candidates for the GGEB to bring to the BGS Admissions Committee and the Chair of BGS. Students are usually notified of the decision of the Admissions Committees by the end of March.

3.2.5 Initiating an Application

Those interested in applying for admission to graduate study should contact the Coordinator:

Ms. Catherine Vallejo
Coordinator, Graduate Group in Epidemiology and Biostatistics
Perelman School of Medicine at the University of Pennsylvania
627 Blockley Hall, 423 Guardian Drive
Philadelphia, PA  19104-6021
Tel: 215-573-3881
E-mail: vallejo@mail.med.upenn.edu

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3.3 Admission Requirements Specific to the Biostatistics Programs

Entering students must have completed at least one year of calculus (including multivariable methods), one semester of linear algebra, and have a working knowledge of a programming language. Previous experience with data analysis and statistical packages is desirable but not required. Advanced courses in mathematics are particularly important for students who intend to pursue the PhD degree.

3.3.1 Applicants from the MS Program

Students in the Biostatistics MS program who seek admission to the PhD program must submit an application.  Typically such students apply in the fall preceding their projected graduation with the MS.  Results on the written qualifications examination are considered in the admission decision (see the section on “Evaluations and Examinations”).

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3.4 Admission Requirements Specific to the PhD Program in Epidemiology

Applicants must demonstrate prior training and experience in epidemiology, clinical sciences, or a public health-related field. This requirement can be satisfied by having a Master’s degree in public health, epidemiology, biostatistics, or related field, OR at least two years of relevant work experience. Individuals admitted without clinical or other biomedical training may be required to take biomedical science courses in addition to the courses required for the PhD in Epidemiology. These courses will not count as electives and must be taken in addition to the required courses and credits. The Admission Committee will determine the need for additional courses at the time of acceptance.

The content of the additional courses required for those admitted without prior clinical or other biomedical training will be determined by a committee consisting of the student’s advisor and two additional epidemiologists who are members of the Graduate Group. The advisor will be responsible for identifying those two faculty members. At least one of the three members of this committee must hold a clinical doctorate and at least one member of the committee must hold a doctorate in epidemiology or a related field, without a clinical doctorate. This committee will identify specific courses to be taken on the basis of a review of the candidate’s academic record/transcripts and research interests, as well as interactions with the candidate. The candidate will be informed of the additional required courses prior to enrollment. It is likely that this additional coursework will increase the amount of time it takes for the candidate to successfully complete the PhD degree requirements.

Combined degree (MD-PhD, VMD-PhD, and DMD-PhD) applicants are exempt from this requirement since they will have had at least two years of relevant coursework in their professional degree program prior to starting coursework for the PhD.

4 Financial Obligations and Support

Tuition costs are determined each year. The Trustees of the University of Pennsylvania reserve the right to increase tuition and fees and to otherwise amend the regulations concerning tuition and fees at any time and to make such changes applicable to students in the University at that time. PhD students receive up to 21 months of funding from BGS. During the initial 21 months, students identify a PhD advisor and work with the advisor and the program to develop a funding plan for the remainder of their graduate program. Most PhD students receive financial support through one or more of the following sources:  assistantships supported by research grants, training grant fellowships, and fellowships from research institutions or private industry. A limited number of teaching assistantships are available.  These sources are described in more detail below. Students who receive full-time support may accept no additional employment during the period of the support. Support for Biostatistics MS students depends on the availability of funds, with priority given to PhD students.

4.1 Financial Aid

The University’s Office of Student Financial Services provides information on student expenses and billing; processes financial aid applications, awards financial assistance; and administers the Penn Plan payment programs.  Students may contact the Office directly at:

Office of Student Financial Services
University of Pennsylvania
Room 100 Franklin Building
3451 Walnut Street
Philadelphia, PA 19104-6270
Tel: 215-898-1988
Email:  sfsmail@SFS.upenn.edu

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5 Resources for Students

5.1 Penn Card

The PennCard is the official identification card of the University of Pennsylvania. The PennCard Center is located on the second floor of the Penn Bookstore, 3601 Walnut Street. A valid, government-issued photo I.D. is required in order to pick up a PennCard. The first PennCard is free. Information about the PennCard and its use is provided at http://cms.business-services.upenn.edu/penncard/home.html.

5.2 PennKey

The PennKey name and password provides access to PennNet, a Penn e-mail account, and many other essential services managed through the PhD Program. All students are required to have a current, active PennKey and password. Students are issued a PennKey Setup Code when they pick up their PennCard.

5.3 The PennPortal

The PennPortal webpage bundles together links to important information for students. To access the PennPortal (https://portal.apps.upenn.edu/penn_portal/portal.php), students should log in with their PennKey name and password. If the “Graduate Students” tab does not automatically appear, students should click on the “My Tabs” button to add the “Graduate Students” tab from the available tabs.

5.4 Black Key

Like all buildings on the Penn medical campus, Blockley Hall is secured through a building-specific black key and/or via your PennCard. The GGEB coordinator will arrange for a black key and PennCard for each student.  Keys are picked up at the security office in the lobby of Stellar-Chance between 11:00 a.m.-1:00 p.m.

5.5 Health Care Coverage

Penn students are automatically eligible for Penn Student Health Services and Chickering Health Insurance. Once a student is matriculated, the University will assume that this health coverage is needed and they will bill for the service. Students who wish to waive the Penn sponsored insurance should log onto PennPortal at http://medley.isc-seo.upenn.edu/penn_portal/portal.php to do so. It is necessary that students watch their bill to ensure that no health insurance fee is incurred. If one is charged to the student account, the GGEB Coordinator should be notified.

5.6 Student Travel Funds

BGS allows doctoral students to apply for partial reimbursement (currently, up to $500/year) for travel to professional meetings if they are making a presentation.  Applicants must justify the expenses prior to attending the meetings.  Dissertation advisors sometimes are able to augment these travel funds. In addition some training grants provide funds for student travel. Information and application provided at: http://www.med.upenn.edu/bgs/travel_funds.shtml

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6 Academic Policies

Students in the PhD program are subject to academic policies of BGS (http://www.med.upenn.edu/bgs/current_students_policies.shtml) as well as the specific policies of the GGEB and PhD program as defined below.

6.1 Code of conduct and academic integrity

6.1.1 Code of General Conduct

All BGS students must conduct themselves at all times in a mature and responsible manner. The rights and property of all persons are to be respected regardless of time or place. For dual degree students (MD-PhD, VMD-PhD), or graduate students who conduct research in a clinical venue, this also includes compliance with rules, procedures and accepted practices in the clinical setting. In addition, BGS students must comply with the University's code of general conduct and other University policies related to student conduct that are described in The Penn Book: Policies and Procedures Handbook of the University of Pennsylvania (http://www.vpul.upenn.edu/osl/pennbook.html). These policies include, but are not limited to, policies on sexual harassment, acquaintance rape and sexual violence, open expression, drug and alcohol usage, and the drug-free workplace. The judicial charter contained within that document is not applicable to BGS students; rather, BGS students are subject to the Charter of Biomedical Graduate Studies Student Judicial System which can be found on the BGS website.

6.1.2 Code of Academic Integrity

The most fundamental value of any academic community is intellectual honesty; accordingly, all academic communities rely upon the integrity of each and every member. Students are responsible not only for adhering to the highest standards of truth and honesty but also for upholding the principles and spirit of the following Code. Violations of this Code include but are not limited to the following acts:

A. Cheating: using or attempting to use unauthorized assistance, material or study aids in examinations or any other academic work, or preventing, or attempting to prevent another from using authorized assistance, material, or study aids.

B. Plagiarism: using the ideas, data or language of another without specific and proper acknowledgment.

C. Fabrication: submitting contrived or altered information in any academic exercise.

D. Multiple Submission: submitting, without prior permission, any work submitted to fulfill another academic requirement.

E. Misrepresentation of Academic Records: misrepresenting or tampering with, or attempting to tamper with, any portion of one's own or any other person's transcripts or academic record, either before or after coming to the University of Pennsylvania.

F. Facilitating Academic Dishonesty: knowingly helping or attempting to help another violate provisions of this Code.

G. Unfair Advantage: attempting to gain unauthorized advantage over fellow students in an academic exercise.

Note that it is the policy of the GGEB that students may collaborate on homework/coursework solutions but must submit their own independent response to any homework assignment. Exceptions to this policy may be made explicitly and in writing by the course instructor.

Given our daily reliance on numerous sources of information, it is essential for faculty and students alike to understand their responsibilities in adhering to the University’s Code of Academic Integrity. To ensure that each student’s work represents the effort envisioned by faculty for a given assignment, these two principles must be observed:
  1. It is essential for faculty to indicate in writing for each assignment the parameters for completing that assignment. This should be a statement of exactly what is allowed and what is not allowed in terms of the use of outside material, consultation with other students or faculty, and the use of material previously created by the student for another course.
  2. Students must be sure they understand the parameters for every assignment. While the instructor is responsible for providing a clear description of these parameters, it is the student’s responsibility to understand them, and to discuss with the instructor any concerns or questions about them

The Penn library website has excellent resources on this topic. The links below provide resources on the specific topic of plagiarism:

http://gethelp.library.upenn.edu/PORT/documentation/plagiarism_policy.html

http://gethelp.library.upenn.edu/PORT/documentation/avoidingplagiarism.html

6.1.3 Code of Clinical Conduct

The relationship of modern biomedical research to the clinical setting may place BGS students in direct contact with patients, patient medical records, or health care workers. BGS students must behave with paramount concern for patients' welfare and with respect for the rights of patients. The expectations of BGS students' conduct in the clinical setting include the following:

A. adherence to appropriate standards of behavior in the presence of patients;
B. adherence to appropriate standards of confidentiality with respect to information about patients;
C. honesty in interactions with clinical colleagues and in recordkeeping;
D. respect for the limits of responsibility and activity set forth by supervisors;
E. appropriate interactions with colleagues and co-workers.

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6.2 Academic standards

6.2.1 Course grades and Academic Probation

Grades for all formal courses are assigned as follows: “A,” distinguished; “B,” good; “C,” unsatisfactory; “D,” poor; “F,” failure. Course directors may award pluses and minuses at their discretion. Grades of B− or above are considered acceptable; grades of C+ or below are unacceptable. A student who receives an unacceptable grade (C+ or lower) in any course is automatically placed on academic probation, an enrollment status that indicates an unsatisfactory level of academic performance. A student who is on probation may take other courses and exams but may not graduate. The probation is automatically lifted when the student has made up the deficient work by receiving an acceptable grade. The student must arrange with the chair of the course in question a program of study that will accomplish this end. One option is to redo the assignments or exams that led to the unsatisfactory grade.

Another is to take the course again during the next semester in which it is offered. In any event, a student who fails to redress the deficiency within one year of being placed on academic probation will be dismissed and considered ineligible for re-admission. If a student receives a second unacceptable grade in another course while already on academic probation, the Graduate Group Chair will convene a committee to review the case. The committee, which will consist of the student’s academic advisor and two other members of the Graduate Group faculty, is authorized to recommend either immediate dismissal or continuation of the probationary status, subject to approval by the Graduate Group Chair and BGS.

6.2.2 Incompletes

In order to graduate, students must satisfactorily complete their course work. There may be times when, for some reason, a student cannot complete the course work within the allotted time. In this case, the student must formally request, in writing, a grade of Incomplete (I) for the course. Requests for Incompletes are not automatically granted, and the course director must agree to enter the grade for that course. Students and faculty should be aware that incompletes become permanent after a period of one year. Thus, course requirements must be completed and a grade reported within one year or the student will not receive credit for the course even though tuition was paid. If the incomplete is not resolved within the one-year period, then the student will be required to take an additional course to complete the requirements of the curriculum. The student must obtain approvals for the replacement course from the advisor and the respective Program Chair prior to registering for it.

6.2.3 Individual Development Plans (IDPs)

BGS requires an annual IDP for all pre-doctoral students (PhD, MD-PhD, and VMD-PhD). The goals of the IDP 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 in their program. Separate forms are used by pre-thesis and thesis level students.Please see https://www.med.upenn.edu/bgs/idp.shtml for specific requirements regarding the IDP and examples of completed IDP forms.

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6.3 Additional Academic Requirements and Policies

6.3.1 Collaborative Institutional Training Initiative (CITI) Training Program

This program is mandatory for all School of Medicine faculty, clinical care associate physicians, physicians at affiliated hospitals, and research staff working with physicians who conduct patient-oriented research.  Researchers conducting clinical studies with federal funding are also required to take human subjects research training.  The Office of the Provost of Research has identified online training devices provided by the CITI program as the accepted standard for fulfilling the requirement for training certification in human research protections. Penn’s IRB requires that researchers conducting clinical trials complete patient-oriented research training, and the CITI program can also fulfill this requirement.

6.3.2 Health Insurance Portability and Accountability Act (HIPAA) training

HIPAA is a federal law that provides for the protection of the confidentiality of patient health records.  All students must complete a University-approved course in HIPAA compliance.

6.3.3 Responsible Conduct of Research

Students are required to take training in the responsible conduct of research (RCR) every academic year. First-year students satisfy this requirement by participating in an on-line Bioethics Symposium. Second-, third-, and fourth-year students attend small-group workshops in which relevant case studies are discussed. Students whose studies extend beyond four years must continue to participate in a yearly training session of their choice. Such students can satisfy the responsible conduct of research requirement by participating in various University-sanctioned bioethics courses and symposia or by serving as an assistant facilitator in a workshop for second-, third-, and fourth-year students.

Faculty must dedicate at least two meetings (1-2 hrs each) per year to RCR training.  To this end, Faculty have access to case studies to use as discussion pieces, in addition to their own resources or examples from their own experience.  The expectation is for these events to be interactive discussions that ideally include all project personnel, but minimally explicitly include all graduate students who work on that project.  After each such event, the Faculty member is expected to fill out the online form found here: http://www.med.upenn.edu/bgs/RCR_FORM.shtml

6.3.4 Course evaluations

Students are requested to submit their feedback promptly and completely at the end of each course throughout their time in graduate training. We take seriously what students say about a course and try hard to improve every year based on students’ feedback.  

Students should also be aware that faculty promotions can be affected by how they are evaluated.  This is not meant to dissuade students from honestly rating the course faculty, but rather as an invitation to take this seriously and be thoughtful about how they rate the faculty’s effort, skill, and teaching abilities.  Constructive criticism is helpful and truly appreciated by both faculty and the graduate group.  Disparaging comments are less helpful and are discouraged. The Program Chairs are always ready to discuss in person any concerns that students may have.

6.3.5 Leaves of absence

During the period prior to dissertation status, the University allows graduate students to take leaves of absence with the permission of the PhD program and BGS. Dissertation level students are allowed leaves of absence only with permission, most notably for medical reasons and for parental leave in association with the birth of a child. Student stipends are suspended during a medical leave period and are re-instated upon return as long as the student is in good academic standing. A student who wishes to take a leave of absence must submit a written request to the Program Chair and the GGEB chair at least one month prior to the beginning of the first semester of the proposed leave. If the leave is for medical reasons, the request must include a note from the student’s doctor. Leaves of absence are granted for no more than one year. The university’s leave of absence policy is provided in the Graduate Catalog Rules and Regulations: http://www.upenn.edu/VPGE/rules.html

6.3.6 Vacation and Time Away

Graduate fellowships provide tuition, fees, health insurance, and a stipend for eligible full-time doctoral students in residence who remain in good academic standing.   A student who accepts a full-time funded position is expected to devote full time to graduate study.

BGS and GGEB offer a 12-month annual training program for funded students. Students are expected to work full-time toward the degree and are entitled to take University and GGEB staff holidays and two weeks per year for personal vacation time. The timing of the vacation must be approved by the supervisor of the entity that provides financial support for the student.  Students who have not yet passed the candidacy exam (see below) must receive permission from the Chair of the GGEB for any additional time away from the University.  A student who has passed the candidacy exam may schedule time away only with the prior approval of his or her dissertation advisor, the individual who is supporting his or her assistantship or traineeship, the Program Chair and the GGEB Chair.

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6.4 Transfer of credit

At least twelve course units must be completed while enrolled in a degree program at Penn; for the PhD degree, a maximum of eight units may be transferred from graduate work done at other institutions. Transfer of credit must be approved by the respective Program Chair, Graduate Group Chair, and the BGS Chair.

6.4.1 Transfer from other graduate groups

Students who are currently enrolled in another graduate group within BGS may apply for transfer into the GGEB by submitting an application for admission to either the PhD Program in Epidemiology or the MS or PhD programs in Biostatistics. Students wishing to transfer must inform their original program of their intent. The student should have the chair of the original program sign a "Transfer of Graduate Group Form" to release the student from the original graduate group and then have the chair of the new program sign the same form to accept the student into the new graduate group. The GGEB will then request that the student's academic file be transferred from the former graduate group office. A similar procedure will be used for students transferring from other graduate programs within the university.

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6.5 Residency, time limits, and fees

Students must complete all course requirements, pass the required examinations, and complete the dissertation within ten years of matriculation. A student who fails to complete the dissertation within the time limit must petition a committee — composed of the student’s academic advisor, the Program Chair (or a designated surrogate if the Chair is also the advisor), and a third member of the faculty designated by the GGEB Chair —to be recertified as a PhD candidate.  The petition must name the student’s dissertation advisor and committee members, describe a plan to finish the research needed to complete the dissertation, and indicate an expected data for the defense and deposit of the dissertation. Should the committee support the petition, it will submit a detailed recertification plan for review and approval by the Director of BGS, as specified in the University-­-Wide Academic Rules for Graduate Degrees.

In addition, PhD candidates must complete the dissertation within five years of passing the Qualifications Examination or being admitted into the PhD program (the latter if admitted to the PhD program after passing the Qualifications Examination at the PhD level as an MS student).  A student who does not complete the degree within five years must petition the GGEB for an extension of the time limit.  The petition must indicate a detailed plan for completing the PhD research, including anticipated dates for defending and depositing the dissertation. The petition will be considered by a committee that includes the student’s academic advisor, the Program Chair (or a surrogate as indicated above) and a third faculty member designated by the GGEB Chair.

A candidate who withdraws from the PhD program after reaching dissertation status and subsequently applies for re-admission must pay the dissertation fees that would otherwise have been due during the withdrawal period.

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7 Graduate Training Programs in Biostatistics

This version of the biostatistics portion of the handbook applies to students who enter the program in the fall of 2015 or thereafter.  For students who matriculated prior to this, please refer to the previous version of the handbook that may be found at http://www.med.upenn.edu/ggeb/GGEB_Handbook.shtml.  Questions about the program for any cohort should be referred to the student’s academic advisor or the Program Chair.

The PhD program in biostatistics is designed to prepare students to be independent researchers in the development of statistical methodologies and in the appropriate and innovative application of these methodologies to biomedical research problems.  In the first five semesters of the program, students complete a series of courses in both theory and applied methodology, engage in individually mentored research experiences, explore statistical collaboration, and complete the qualifications examination.  Within this period, students also identify a dissertation research problem and an advisor and present a research proposal as part of the candidacy examination.  Students typically defend their dissertations and graduate within five years of matriculation.

The MS program is designed to prepare students to be practitioners of biostatistical methodologies.  Some MS students may move to enter the PhD program.  The MS program closely parallels the first two years of the PhD program and requires four full-time semesters of course work, exploration of practical aspects of collaboration, and an independent research project which serves as the MS thesis.

7.1 Elements Common to MS and PhD Programs

7.1.1 Academic Advisor

Each incoming student is assigned an academic advisor who serves as the student's primary mentor, advising in course selection and related academic matters.  The program attempts to match students to advisors who have similar backgrounds and interests.  A student may change advisors at any time by request to the Program Chair.  A PhD student’s dissertation advisor, once selected, assumes the role of academic advisor during the later years of study.  Furthermore, at any time a student may refer questions about his or her program to the chair of the Academic Advising Committee.

At the beginning of the academic year, each student, in collaboration with his/her advisor, prepares a proposed academic program, the Individual Development Plan (IDP), including courses to be taken, courses to be transferred, and timelines for examinations and dissertation preparation.

7.1.2 Non-Credit Requirements

The department hosts a weekly biostatistics research seminar that invites speakers from other universities, industry, and government.  All students are expected to attend at least six seminars per semester, provided there is no conflict with courses.  Other non-credit requirements include Responsible Conduct of Research, CITI, and HIPAA training.  These requirements are described in detail in Section 6.3.  Biostatistics in Practice I and II, as well as, for PhD students, serving as a teaching assistant, are also non-credit requirements (see Sections 7.3.9 and 7.5, respectively).

7.1.3 Transfer of Credit

Only courses considered at the graduate level may be transferred from previous training.  At least eight course units of the total program required for the MS degree must be completed while enrolled in a graduate program at UPenn.  Because the MS program requires only 12 total course units, no more than four may be satisfied by transfer credit.  Similarly, at least twelve course units of the twenty required for the PhD degree must be completed while enrolled in a degree program at UPenn; thus a maximum of eight units may be transferred from graduate work.  Courses proposed for transfer credit must be relevant to training in biostatistics and may include courses in theory, methods, or towards a minor (see Section 7.3.6 regarding minors).  Transfer of credit must be approved by the Program Chair and the GGEB Chair.

7.1.4 Auditing

Auditing a required course is routinely allowed for students who are transferring credit for that course.  In all other cases, auditing of a course is strongly discouraged.  If a student wishes to audit a course he/she must consult their academic or dissertation advisor, the course director, and prepare a written request to the Program Chair explaining reasons for the proposed course audit.

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7.2 Master of Science (MS) in Biostatistics

7.2.1 Course Requirements

Candidates for the MS degree must complete 12 units of course credit, pass the written qualifications exam, and prepare a Master’s thesis.  Required courses cover probability, mathematical statistics, and statistical methods including categorical data analysis, linear models, survival analysis, and applied data analysis.  All students also take a course in epidemiology.

The MS in Biostatistics typically requires four semesters of formal course work.  Students must complete nine units of required courses, three units of electives, and the Biostatistics in Practice I and II requirements (see Section 7.3.9). The required courses are described below.  The courses in bold type are the “core” courses for the MS degree that are covered on the written qualifications examination.

Theory:

BSTA 620 Probability (1 unit)
BSTA 621 Statistical Inference I (1 unit)

Methods:

BSTA 630 Methods I (1 unit)
BSTA 632 Statistical Methods for Categorical and Survival Data (Methods II) (1 unit)
BSTA 651 Introduction to Linear Models & Generalized Linear Models (1 unit)
BSTA 656 Longitudinal Data Analysis (1 unit)
BSTA 660 Design of Observational Studies (1 unit) OR BSTA 661 Design of Interventional Studies I (1.0 unit)
BSTA 670 Statistical Computing (1 unit)

Applications:

BSTA 509 Introductory Epidemiology (0.5 unit)
BSTA 510 Introduction to Human Health and Diseases (0.5 unit) Note:  This course will not be required nor offered for students matriculating after 2016
BSTA 511 Biostatistics in Practice I (0.5)

7.2.1.1 Electives

Students in the MS program choose three additional units from a list of advanced courses in biostatistics and related topics.  At least two of these courses must be quantitative; the third may be in a related scientific field subject to approval by the Curriculum Committee Chair and Program Director.  A partial listing appears under the section on electives for the PhD program (Section 7.3.3).  In addition to these electives, BSTA 622 Inference II and BSTA 754 Advanced Survival Analysis, which are required courses for the PhD program, may be used as advanced electives for the MS program.  Courses not described here may be used as advanced electives for the MS program upon receiving approval from the Chair of the Curriculum Committee and the Program Chair.

7.2.2 Biostatistics in Practice and the MS Thesis

All MS students must participate in Biostatistics in Practice I and complete a Biostatistics in Practice II project, which serves as the MS thesis.  The project may be completed in any semester.  See the description of the Biostatistics in Practice requirements in Section 7.3.9.

7.2.3 Typical Course Sequence for Full-Time Students in the MS Program

 

  Semester Required Credit Courses (units)

 

 

 

 

Year 1

Fall

BSTA 620: Probability (1)
BSTA 630: Statistical Methods and Data Analysis I (1)
BSTA 509: Introductory Epidemiology (0.5)
BSTA 510: Introduction to Human Health and Diseases (not required or offered after 2016)
BSTA 511: Biostatistics in Practice I (0.5)

Spring

BSTA 621 Statistical Inference I (1)
BSTA 632 Statistical Methods for Categorical and Survival Data
BSTA 651 Introduction to Linear Models & GLM (1)
BSTA 511: Biostatistics in Practice I (cont.)


Summer


Written Qualifications Examination

 


 

Year 2

Fall

BSTA 670 Statistical Computing (1)
Advanced Electives (2)

Biostatistics in Practice II / MS Thesis

Spring

BSTA 656 Longitudinal Data Analysis (1)
BSTA 660: Design of Observational Studies (1) or BSTA 661: Design of Interventional Studies (1)
Advanced Elective (1)

Biostatistics in Practice II / MS Thesis Presentation

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7.3 Doctor of Philosophy (PhD) in Biostatistics

7.3.1 Funding Policies

Full-time PhD students are eligible for funding in the form of traineeships, fellowships, and research and teaching assistantships.  The work associated with these sources of support is an essential part of the graduate training program.

At the beginning of the academic year, each funded student receives a letter describing sources of support and associated obligations.  All doctoral students admitted to the program receive support from BGS for up to 21 months. During this time students take courses and explore research opportunities with faculty in the department.  Once students decide on a dissertation advisor, the advisor, the student and the Program chair will work to develop a sustained funding plan that will cover the student’s time during the remainder of their graduate program. A number of funding opportunities are available including federally funded research and training grants, partial TAships and funding through partnerships with industry. The typical length of time in the program is five years.  Students in good academic standing have occasionally received funding for up to six years in the program.

7.3.2 Course Requirements

The PhD in Biostatistics typically requires five to six semesters of coursework and additional semesters devoted to dissertation research.  This is usually accomplished in four to five years of full-time study.  The standard course sequence for PhD students consists of 3 units in theory, 7 units in statistical methods, 0.5 unit of epidemiology, 0.5 unit of Biostatistics in Practice I, 2 units toward a minor and 4 units of electives in advanced theory and methods. In addition, a minimum of three units of credit including one unit of independent study (BSTA 999), two units of guided research (BSTA 920 and BSTA 995) and three semesters of lab rotations (BSTA 699) are required.  In general, students are expected to have completed all required courses by the end of their 4th year (or equivalent for those who enter with Master's degrees).  In rare cases substitutions may be made.  Such alternatives must be pre-approved by the chair of the Curriculum Committee, the Program Chair, and the director of the course being waived, who is in the best position to evaluate whether the necessary skills are met by the substitution.

Below are the required core courses; the courses in bold type are PhD “core” courses that are covered on the written qualifying examination.

Theory:

BSTA 620 Probability (1 unit)
BSTA 621 Statistical Inference I (1 unit)
BSTA 622 Statistical Inference II (1 unit)

Methods:

BSTA 630 Statistical Methods and Data Analysis I (1 unit)
BSTA 632 Statistical Methods for Categorical and Survival Data (Methods II) (1 unit)
BSTA 651 Introduction to Linear Models & Generalized Linear Models (1 unit)
BSTA 656 Longitudinal Data Analysis (1 unit)
BSTA 660 Design of Observational Studies (1 unit) OR BSTA 661 Design of Interventional Studies I (1.0 unit)
BSTA 670 Statistical Computing (1 unit)
BSTA 754 Advanced Survival Analysis (1 unit)

Applications:

BSTA 509 Introductory Epidemiology (0.5 unit)
BSTA 510 Introduction to Human Health and Diseases (0.5 unit) Note:  This course will not be required nor offered for students matriculating after 2016.
BSTA 511: Biostatistics in Practice I (0.5)

7.3.3 Electives and Independent Study

Students are required to take 4 additional advanced electives; a partial listing of such courses is given below.  In addition to this list, other courses offered by departments outside of Biostatistics and Epidemiology may be appropriate advanced electives and may be used as an advanced elective for the PhD program upon receiving approval from the student’s academic advisor and the Program Chair.  Independent study or reading courses (BSTA 999) are reserved for doctoral students who have passed the written qualifications examination and are either choosing a dissertation topic or undertaking the early stages of dissertation research.  At most one of the four required advanced electives may be a reading course, and only on a topic not offered as a formal course with a year.

STAT 520 Applied Econometrics I (1 unit)
STAT 521 Applied Econometrics II (1 unit)
STAT 530 Probability (1 unit)
STAT 531 Stochastic Processes (1 unit)
STAT 921 Observational Studies (1 unit)
STAT 925 Multivariate Analysis: Theory (1 unit)
STAT 974 Modern Regression (1 unit)
OPIM 930 Stochastic Models II (1 unit)
BSTA 771 Applied Bayesian Analysis (1 unit)
BSTA 774 Statistical Methods for Evaluating Diagnostic Tests (0.5/1 unit)
BSTA 775/STAT 920 Sample Survey Methods (1 unit)
BSTA798/799 Advanced Topics in Biostatistics (0.5/1 unit)
BSTA 782 Statistical Methods for Incomplete Data (1 unit)
BSTA 783 Multivariate and Functional Data Analysis (1 unit)
BSTA 785 Statistical Methods for Genomic Data Analysis (1 unit)
BSTA 786 Advanced Topics in Clinical Trials (1 unit)
BSTA 787 Methods for Statistical Genetics in Complex Human Disease (1 unit)
BSTA 788 Functional Data Analysis (1)
BSTA 789 Big Data (1)
BSTA 790 Causal Inference in Biomedical Research (1 unit)
BSTA 820/STAT 552 Statistical Inference III (1 unit)
BSTA 852/STAT 910 Forecasting and Time Series (1 unit)
BSTA 854/STAT 927 Bayesian Statistical Theory and Methods (1 unit)

7.3.4 Applied Research Requirement, Equivalent of MS Thesis

All PhD students must participate in Biostatistics in Practice I and complete a Biostatistics in Practice II project, a requirement that students typically satisfy during the first or second year.  See Section 7.3.9 for further details.

7.3.5 Teaching Practicum

All students in the PhD program must provide teaching support for a course or courses offered by the Department of Biostatistics and Epidemiology or related programs.  This is discussed in detail in Section 7.5.

7.3.6 Minor

Students must complete a two-unit minor sequence in one or more areas of science relevant to biomedical research. Some possible subject areas for minor courses include epidemiology, genetics, biology, psychology, economics, computer science, and bioengineering. Minor courses are typically taken outside of the GGEB, with the exception of advanced epidemiology courses (beyond BSTA 509) which may also be counted toward the minor. The two-unit minor sequence must be approved by the curriculum committee chair and the program chair.

7.3.7 Examinations

The PhD program requires the successful passing of three examinations: the written Qualifications Evaluation, the oral Candidacy Examination, and the Dissertation Examination.  Later sections outline the procedures for each of these.

7.3.8 Lab Rotations

Goals and Objectives

The overall goal of the rotations is to expose students to biomedical research, and in particular research related to statistical methodology early in their training.  In addition, students will rotate through a number of different labs, in order to get a broad perspective on research and faculty.   This will also assist the students in identifying their research interests and thesis topic earlier in their educational process.  In addition, both the students and faculty can assess whether they are a good match for possible dissertation advisor/advisee relationships. By the end of 21 months of training (summer of year 2) students who were initially funded by BGS funding will identify their dissertation advisor, have a foundation for the first topic in their dissertation work, and move off of BGS funding and onto funding that is related to their dissertation work (ideally). Students will normally identify their PhD mentor through working with them on a lab rotation.  Students who are funded by a training grant during their first 21 months in the program will remain on the training grant throughout their program.  Students who are currently funded or who have interests in receiving funding during their dissertation research from a training grant should discuss how to structure their lab rotations with the training grant director. Lab rotations that offer research experience in areas relevant to our training grants will be available each year.

Lab Rotation Content

Laboratory rotations should focus on statistical research as opposed to simple data analysis or service/project work.  Ideas include implementation of a method from the literature, literature review of methods, running and summarizing simulations, or the analysis of a complicated dataset.  It is recognized that, depending upon the background of the students matriculating into the program, the first lab rotation may need to be a lighter introduction to the methodological area such as focusing on literature review, study design, logistics, and data management and/or data analysis.

Duration and Number of Individual Rotations and Dissertation Advisor Choice

Students are expected to participate in 3-5 rotations in total.  First year students will have 3 rotations: fall, spring, and summer.  Students can expect to spend 20+ hours per week during the fall/spring semesters and full time 40+ hours during the summer.  In the second year it is expected that students will settle into a relationship with a potential PhD dissertation advisor with the goal of focusing their research in an area of research related to that of the advisor.  Nevertheless, if needed, a fourth or even fifth lab rotation may occur in the second year to help the student decide on a research topic.  In many cases the MS thesis (Biostatistics in Practice II project) will be related to the dissertation for a PhD student.  In addition to determining an area of research interest, the dissertation advisor must show willingness to, at least partially, support the student.

Laboratory Rotation Assignments (i.e. match making)

Prior to the arrival of the new students, interested faculty mentors will submit a short summary describing their proposed laboratory rotation (similar to a course description).  During new student orientation and the first week of classes, faculty who are interested in serving as a mentor for the upcoming semester will make a brief presentation of their projects.  Faculty mentors can also distribute a handout with a more detailed project description to interested students.  Next, the students will rank their choice of projects and the rankings will be reviewed by members of the Academic Advising Committee.  Each student will be encouraged by the committee to meet with individual faculty of 2 or 3 potential collaborations.  This should occur within a short period of time so that assignments can be made and begin in a timely fashion for the Fall semester.  After those meetings, participating biostatistics faculty will also rank their student preferences.  The Academic Advising Committee will take this information and facilitate matching students to faculty.  It is important to note that each student will be working in three labs during their first year, so students and faculty will have ample opportunity to work with each other over the course of the program and initial matches do not preclude options for other collaborations.  It is the responsibility of faculty mentors to make sure any required IRB approvals are obtained, and that students have the requisite CITI training to work with any data related to their laboratory rotation project.

Evaluation

At the initiation of each new lab rotation, the advisor and mentee will write a short summary of the goals and expectations for the particular laboratory rotation.  This document will be submitted to the Academic Advising Committee.  Laboratory rotations are taken for credit (1 unit per semester, BSTA 699) and students receive both a written evaluation and a letter grade.  Summer rotations also receive a letter grade; however, these will not appear on the formal transcript.  In addition, each student will present a 20-minute (shorter for 1st rotation) oral presentation of their laboratory rotation work twice per year during a brown bag format “chalk talk”.  Attendance will be required for all students participating in various lab rotations and encouraged for upper class students as well as faculty.

7.3.9 Biostatistics in Practice I and II

Biostatistics in Practice I Workshop

Participation in Biostatistics in Practice I is required for both the MS and PhD degrees.  This year-long 0.5 course covers practical aspects of utilizing biostatistics in multi-disciplinary research teams.  Didactic lectures address both the substantive and communications aspects of consulting, with student participation in class discussions considered critical.  In addition, each student attends 2-3 consulting sessions between a biostatistics faculty member and his/her collaborators.  For PhD candidates, Biostatistics in Practice I may be waived if the student 1) has previously achieved an MS in Biostatistics or Applied Statistics and 2) can demonstrate exposure to an equivalent curriculum in their previous degree program.  Such a waiver requires the approval of the Program Chair.

Biostatistics in Practice II Project

The Biostatistics in Practice II project offers the student an opportunity to acquire and demonstrate proficiency in statistical collaboration and data analysis.  The project is defined by several elements:  A scientific question or hypothesis arising in medical research; the statistical methodology needed to address the question; the development of a study design and/or analysis of a relevant data set; and a summary of the results of these analysis. In most cases, a collaborating medical scientist provides the research question and the data.  The student, under the supervision of a biostatistics faculty member, identifies the appropriate statistical methods and conducts the analysis.  The analysis should be sufficiently extensive and detailed to support a manuscript publishable in the medical literature.

The project consists of two parts.  The first is a written report including:  a description of the research question; a short statement of background and significance; a description of the statistical methods applied; the results of the analysis; and summary of the major findings and conclusions.  The second is a short (15 minute) oral presentation of the project to the biostatistics faculty and students.  For students wishing to use the Biostatistics in Practice II project as the Master’s Thesis (see below) the written report should describe the study in a format suitable for publication in a scientific journal. For students not pursuing the MS degree, slides used to accompany the oral presentation may be submitted as the written report.

Students register for Biostatistics in Practice II by indicating to the Administrative Program Coordinator that they intend to complete the requirement over the next two semesters (see https://dbe.med.upenn.edu/biostat-research/resources-educational for details).  The project must be completed by the end of the following April for students who sign up in the fall semester, or by the end of the following August for students who sign up in the spring semester.

All data analyses done as part of the Biostatistics in Practice II project must have IRB approval.  In most cases this requirement is satisfied if the research objectives are part of an existing protocol of the participating medical research collaborator, as long as the student is added to the protocol according to the standard modification procedures required by the IRB.

7.3.10 Typical Course Sequence for Full-Time Students in the PhD Program:

 

Semester 1

Funds

Plans

 

 

 

 

Year 1

Fall

BGS

BSTA 620 Probability (1)
BSTA 630 Statistical Methods and Data Analysis I (1)
BSTA 509 Introductory Epidemiology (0.5)
BSTA 510: Introduction to Human Health and Diseases (not required or offered after 2016)
BSTA 511: Biostatistics in Practice I (0.5)
BSTA 699: Lab Rotation

Spring

BGS

BSTA 621: Statistical Inference I (1)
BSTA 632: Statistical Methods for Categorical and Survival      Data (Methods II) (1)
BSTA 651: Linear Models and Generalized Linear Models (1)
BSTA 511: Biostatistics in Practice I (cont.)
BSTA 699: Lab Rotation

Summer
BGS

Written Qualifications Examination

            BSTA 699: Lab Rotation

 

 

 

 

Year 2

Fall

BGS

BSTA 622: Statistical Inference II (1)
BSTA 670: Statistical Computing (1)
BSTA 754: Advanced Survival Analysis (1)
BSTA 699: Lab Rotation

Biostatistics in Practice II / MS Thesis

Spring

BGS

BSTA 660: Design of Observational Studies or BSTA 661: Design of Interventional Studies (1)
BSTA 656: Longitudinal Data Analysis (1)
Advanced Electives (1)
BSTA 699: Lab Rotation

Biostatistics in Practice II / MS Thesis Presentation
Summer

BSTA

Oral Candidacy Examination
PhD Thesis*

 

 

 

 

Year 3

Fall

BSTA

BSTA 999: Independent Study (1)
Advanced Electives (1)
Minor (1)

Oral Candidacy Examination (if not completed in summer)
F31 Grant Proposal
PhD Thesis

Spring

BSTA

BSTA 920: Guided Dissertation Research (1)
Advanced Electives (1)
Minor (1)

F31 Grant Proposal (if not completed in fall)
PhD Thesis

Summer

BSTA

PhD Thesis

 

Years 4-5

Fall
BSTA

BSTA 995: Dissertation Research (1)
Advanced Electives (1)

PhD Thesis

 

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7.4 Evaluation and Examinations

Evaluation for the MS degree is based on performance in the required and elective courses, successful performance on the written Qualifications Examination, and completion of the MS thesis/Biostatistics in Practice II project.  Evaluation for the PhD degree is based on these criteria plus ongoing interactions with the faculty advisor(s), laboratory rotations, performance on the Candidacy and Dissertation Examinations, and the dissertation itself.

7.4.1 The Written Qualifying Examination (MS and PhD)

The following guidelines refer to the written Qualifications Examination required of all MS and PhD students in Biostatistics.  The Qualifying Examination Committee develops and administers the examination each year and presents the results to the full faculty.

Passing of the written Qualifications Examination is required for continuation in both the MS and PhD programs.  This examination also satisfies the UPenn examination requirements as outlined below.  Students in both programs take the same exam although there are different possible outcomes.

7.4.2 MS Program Examination Requirements

For students in the MS program in Biostatistics, the written qualifying examination plays the role of the University-required “General Examination” defined in the Graduate Studies catalog under the MS degree as follows:

General Examination: A general examination by the graduate group in the major subject is required in addition to all other examinations.  The purpose of the general examination is to test the candidate's knowledge of his or her major subject in its broader aspects as well as proficiency in the particular courses he or she has taken. This examination may be oral, or written, or both, as the graduate group may decide.  The mere satisfaction of minimum requirements does not entitle the student to be admitted to this examination. The examination covers the topics in the eight “core” courses listed in the “training Programs” section. The exam consists of two sections:  Part A (Theory) and Part B (Methods). Students must attempt both Part A and Part B on their first attempt. For doctoral students, failure to do so will result in an automatic grade of Fail on the section not attempted; for MS students failure to do so will result in an automatic grade of Fail on both parts of the exam

7.4.3 PhD Program Examination Requirements

The written Qualifications Examination serves as the university-required “Qualifications Evaluation” as defined in the Graduate Studies catalog.  PhD students must pass the written Qualifications Examination as the first step toward full PhD candidacy.  The examination is offered each summer, as possible in June to allow for grading and faculty review such that students will have results before the July 4th holiday each year.  All full-time PhD students are expected to sit for the examination after their first year of study, with the option to retake the exam the following year if needed.  No student is allowed to take either part of the exam more than twice.

The exam consists of two parts: theory (“Part A”) and methods (“Part B”).  Students are given a grade on each part, and have up to two opportunities to take each part.  A student must receive a passing score at the PhD level on both parts of the exam to be considered to have passed.  Because the exam is offered only once a year, PhD students who do not pass one or both parts of the exam and elect to take it a second time have the opportunity to take two additional semesters of course work between examinations.  A PhD student who passes one part of the exam at the PhD level is not required to take that part a second time. 

7.4.4 Examination Results and Notification

All matters pertaining to grading and review of the written qualifications examination by the faculty are confidential, but some general procedures are outlined here.

Once grading is complete (typically two weeks after the exam), the faculty of the Biostatistics program meet to review the examination.  The meeting also provides an opportunity to review the progress of all students in the program such that grades, performance in lab rotations, and related materials may also be discussed in addition to the exam scores.  Because the difficulty of the examination may vary from year to year, there are no absolute cut-offs for passing.

For an MS student the examination has two possible outcomes: pass at the MS level or fail.  An MS student who fails must pass a supplementary oral examination (see below) in addition to completing any other requirements for the MS degree.

MS students will also be separately evaluated for the outcomes described below for PhD students and notified if they have passes one or both parts at the PhD level.  Applicants to the PhD program should note that outcomes 1 or 2 do not guarantee admission into the PhD program.  For MS students admitted to the PhD program, the outcome on the first attempt of the exam as an MS student is retroactively considered to be equivalent to the first attempt as a PhD student (see above).

For a PhD student, the examination has four possible outcomes:
  1. Pass at the PhD level.
  2. Pass only Part A (Theory) or only Part B (Methods) at the PhD level.
  3. Pass at the MS level.
  4. Fail.

A PhD student who achieves outcome 1 is eligible to continue working to complete other PhD program requirements and, in particular, should begin the process of selecting a dissertation topic and advisor.  As described below, the oral Candidacy Exam is required within 18 months of the successful completion of the written qualifications examination.  Students will be strongly encouraged to take it the summer or early fall of the year after passing the written Qualifications Examination, especially if they have identified a topic/advisor through their lab rotations.  (Students who do not meet this deadline will be on "academic probation".)

A PhD student who achieves outcome 2 must re-take and pass the failed part at the next opportunity in order to continue in the PhD program.  A PhD student who achieves outcomes 3 or 4 must re-take the entire exam, and pass both parts, at the next opportunity in order to continue in the PhD program.  A PhD student who achieves outcome 1, 2, or 3 may complete the requirements for the MS degree.  A PhD student who achieves outcome 4 and wishes to earn an MS degree must pass a supplementary oral exam (described below).

Each student who takes the exam receives written notification of his or her outcome as soon as possible after the faculty grading meeting.  No other information is made available before that time.  The letter notifies the student of the outcome of the exam, recommendations for continued study, and the process for discussion of the exam with the QEC.

Supplementary Oral Examination for Students Seeking an MS Who Fail at the MS Level

This oral examination is administered by a committee made up of three faculty members selected by the Chair of the Qualifying Examination Committee in consultation with the student’s academic advisor.  This supplementary oral exam should take place no later than the end of the fall semester following the distribution of the results of the written qualifying exam.  This examination is separate from the required presentation of MS thesis work (Biostatistics in Practice II) that is open to all students and faculty.

This oral examination is closed.  In order to provide focus for both the student and the exam committee, the examination begins with a brief presentation (no more than 20 minutes) by the student of the MS thesis.  The examination then focuses on methodology and applications related to the MS thesis. 

The faculty examination committee makes one of three recommendations for each student:  pass, conditional pass, or fail.  A student who successfully passes is eligible to continue in the MS program.  A conditional pass may be selected if the committee believes that there are specific weaknesses that can be addressed in a short time by the student.  For this option, the committee members must identify the area(s) of weakness, as well as specific remedies and a time frame for satisfying the conditions.  Possible remedies include, but are not limited to, repeat of the oral exam at a later date, writing a paper on a topic in statistics, or writing a paper on a data analysis covering the specific area(s) identified as requiring improvement.  The committee evaluates this work and makes a recommendation of pass or fail.  The student must satisfy the conditions of the pass within three (3) months of the oral exam.  A student who fails the oral examination is not eligible to receive the MS degree.

7.4.5 MS Students Applying to the PhD Program

Students enrolled in the MS program who wish to apply to the PhD program must submit a formal application.  As the written qualifications examination is typically administered in the summer after the first year of study, it is likely that the results will be known to the Admissions Committee.  The Admissions Committee determines how to use the results of the written examination in the admissions process.

MS students who pass both parts of the written qualifying examination at the PhD level on the first attempt and are admitted to the PhD program are not required to take a second examination.  MS students who pass one or both parts at the MS level and are admitted to the PhD program are required to take the deficient part of the examination a second time and pass at the PhD level in order to continue in the PhD program. 

7.4.6 Review of the Examination

A student who does not pass one or both parts of the examination at the intended level may request to review his/her exam paper with the Qualifying Examination Committee (QEC) chair and, optionally, his/her academic advisor.  The purpose of such a review is to help the student evaluate the types of mistakes made, identify areas where further study is needed, etc.  The QEC retains the graded exam papers and does not return them to the students.

A student may appeal the outcome of the qualifying examination to the QEC Chair, who together with the QEC membership evaluates the appeal and judges whether it has merit.  A grade can only be changed in cases of a specific error in scoring.  The QEC refers any grade change that could affect the student’s exam outcome to the full Biostatistics faculty, who decide whether to revise the exam outcome.

Because a minor revision of the score is unlikely to change the exam outcome, a student should only initiate a formal appeal if there were one or more egregious errors in the problem or in its grading, the correction of which would likely lead to a substantial increase in the score.  The QEC Chair can advise the student on the prospects for success of a proposed appeal.  A student who seeks a formal review must request it, in writing, from the QEC Chair within one week of the issuance of the letter notifying the student of the exam result.

7.4.7 Sickness Policy

A student who has declared an intention to sit for the exam, but at the time of the exam is too ill to attend, may request a deferment by contacting both his/her academic advisor and the Chair of the QEC.  A deferment can be granted only if the student provides a note from a medical doctor excusing him or her from the exam as a result of the illness.  The student may then be allowed to take the exam on or before the first business day when the note indicates that the student may return to work.  The decision to request a deferment must be made before taking the exam.  A student who takes any part of a day’s exam will be considered a complete exam and graded accordingly.

7.4.8 The PhD Candidacy Examination

In order to advance to candidacy for the PhD degree in Biostatistics, a student must successfully pass a candidacy examination.  This examination satisfies the requirements of the University’s required “Candidacy Examination” defined in the Academic Rules on the Provost website: https://provost.upenn.edu/policies/pennbook/2013/02/13/academic-rules-for-phds-and-research-master-s-degrees

The purpose of the candidacy examination is to evaluate whether the student is qualified to proceed to dissertation research.  Although the examination is structured around the dissertation proposal, it may also cover any material in the student’s course work.  This includes the core courses and other requirements, as well as the minor courses.  The examination should emphasize the student’s qualification to continue as well as the content of the dissertation proposal.  Committee members are encouraged to communicate to both the student and the dissertation advisor suggestions regarding the proposed research, as well as the feasibility of completing the project in a reasonable time.

Candidacy Examination Committee Membership

The student’s candidacy examination committee must include

a) the student’s dissertation advisor, who must be a member of the GGEB
b) a second Biostatistics faculty member
c) either a third Biostatistics faculty member or a Statistics Department faculty member
d) an expert in the applied content area of the proposed dissertation

At least one member of the committee must be a faculty member outside of the GGEB.  This can be a Statistics faculty member who does not hold a GGEB appointment, the content area expert, or an additional (fifth) member of the committee.  At least half of the committee members must be from the GGEB.  The candidacy exam committee chair and members are nominated by the dissertation advisor, subject to approval by the Program Chair and the GGEB chair.  The candidacy committee must be approved in advance of scheduling the candidacy exam.  The committee chair is a voting member who is responsible for chairing the candidacy exam.  The student’s dissertation advisor may not be the committee chair.  All dissertation committee members must attend the candidacy exam in person.

The student’s candidacy exam committee typically continues as the dissertation committee.  Changes to the committee must be approved by the Program Chair and the GGEB chair.

Candidacy Examination Scheduling

To maintain good academic standing, students must advance to candidacy by 18 months after passing their written qualifications examination.  In typical cases this will occur no later than the beginning of the student’s fifth (spring) semester, although students are encouraged to complete their candidacy examination with one year of passing the written qualifications examination.  It is the responsibility of the dissertation advisor to work with the student to schedule the candidacy exam once the dissertation research has been clearly outlined.  The Program Chair will schedule the candidacy examination for any student who has not met this deadline.

Content of the Dissertation Proposal

The student should provide a written dissertation proposal to the committee at least two weeks prior to the scheduled examination date.  The members review the proposal and prepare questions for the exam.

The dissertation proposal should include a review of the literature relevant to the topic to be studied.  The proposal may, but need not, include preliminary research results.  The paper should be primarily a true proposal and should typically not exceed twenty pages.

The examination lasts up to two hours and typically includes three parts:  First, the student gives a formal presentation of the proposal, generally not to exceed 45 minutes (which may be extended if there are questions during the talk).  Next, committee members question the student on the proposal or on topics in biostatistics or the minor.  Once all committee members are satisfied that the questioning is complete, the student is asked to leave the room.  The committee then discusses the examination, votes the outcome (see below), and makes recommendations (if any) for future research and study.  The student is then readmitted and informed of the outcome.  The committee chair ensures that necessary forms are signed and returned to the graduate program office.

Candidacy Examination Outcomes

The candidacy exam has three potential outcomes:

Retaking the Candidacy Examination

A student who fails the candidacy exam after taking it a second time, or who does not make a second attempt within six months of the first (unsuccessful) attempt, is automatically withdrawn from the program.

A student who has passed the candidacy exam but wishes to change dissertation topics must prepare a new proposal and submit it to his or her committee.  A discussion of the new proposal should be scheduled within three months of its submission.  If there is no substantial change in the statistical content area, the candidacy exam need not be retaken, and the committee need not be reconstituted.  If there is a substantial change in the statistical content area, the full committee determines whether an additional candidacy exam is required.  The student, the advisor for the new proposal, and the other members of the committee also decide on any changes in the composition of the committee.

7.4.9 Review of “Lab Notebook”

BGS mandates that the student’s dissertation committee review the student’s “lab notebook” at each of its meetings.  The Biostatistics PhD program interprets this to mean that the student should make available for faculty review, upon request, primary documentation of any substantial element of the dissertation.  Such a review takes place at the candidacy exam and any subsequent meetings of the committee, and following the closed session of the dissertation defense.  Examples of materials subject to review include the statement and formal proof of a key theorem; the code and results of a simulation study; or the data, code and results of a data analysis.  Prior to the meeting, the student’s advisor, in consultation with the dissertation committee, designates a short list of such items that the student makes available in electronic or hard-copy format. The committee chair sets aside time at the meeting for the review of this material. In keeping with the BGS policy, there is no expectation that the committee should scrutinize all such documents “in their entirety”; rather, the review should be sufficient to satisfy the committee that the student’s research records are “complete and well managed”.

7.4.10 Frequency of Dissertation Committee Meetings

Once a student has advanced to candidacy, his/her dissertation committee must meet at least once every six months to review goals and progress.  A review of the “lab notebook” (see above) must accompany each such meeting.  The advisor, working with the chair of the committee, schedules the meetings.  The student is responsible for providing any review materials needed by the committee in a timely fashion, typically at least two weeks before a meeting.

7.4.11 PhD Dissertation Examination

This section provides guidelines for the content of the dissertation and the format of the defense. The Biostatistics Program follows the regulations described by BGS. The final steps toward the PhD degree are the preparation of an acceptable dissertation and the dissertation defense.  Refer to the Academic Rules on the Provost website: https://provost.upenn.edu/policies/pennbook/2013/02/13/academic-rules-for-phds-and-research-master-s-degrees

Permission to Write and Defend the Dissertation

The dissertation committee must formally grant permission to write the thesis.  Students must submit the thesis to the graduate group within six months of receiving permission to write.

If the student will not meet the six-month deadline, s/he 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 program or offered a terminal masters degree.

After the student submits the thesis, the committee has up to one month to review it.  If the committee determines that the student must revise the thesis prior to defending it, the student will have one month to make the revisions.

Once the committee approves the thesis, the student will have one month in which to finalize the defense arrangements.  It is expected that the student will make tentative arrangements for the defense before this point.

Students Leaving the Department Prior to Defending the Dissertation

Refer to http://www.med.upenn.edu/bgs/dissertation_policies.shtml

Dissertation Level Students Changing Mentors

Refer to http://www.med.upenn.edu/bgs/dissertation_policies.shtml

Scheduling

The dissertation defense should be scheduled when the candidate and the dissertation advisor agree that the research is near completion and the draft dissertation is in a format suitable for distribution to the committee.  As soon as a date and time are fixed, the graduate program coordinator reserves a room (for at least two hours) and prepares the necessary public announcements.  In order to accommodate space and scheduling constraints, the date of the exam should be set at least one month before it will take place.  All dissertation committee members must attend the exam in person.

Content and Format of the Dissertation

A typical dissertation consists of five chapters: The first is an introduction and brief literature review; in many cases, this is similar to the dissertation proposal. The next three cover the three main topics of the dissertation; these may be written in a format suitable for submission as individual articles to peer-reviewed journals. The final chapter summarizes the dissertation findings and indicates possible future research directions. There are no upper or lower limits on the length of the document. It is the expectation that at least two of the three middle chapters will be methodological and have been submitted to peer-reviewed journals at least two weeks prior to the dissertation defense. Exceptions to this submitted paper requirement would need prior approval from the dissertation committee and the Director of the Graduate Program.

Content and Format of the Defense

At least four weeks prior to the exam, the student should provide each committee member with a copy of the full dissertation.  The committee members review the dissertation and prepare exam questions based on it.  The defense consists of two parts:

  1. Open session.  The chair describes the process to all attendees and introduces the candidate. The candidate then presents his/her research in the style of a departmental colloquium. Typically, the candidate presents one chapter in depth, with a very brief overview of the others. This presentation should not exceed 45 minutes.  At the close of the formal presentation the candidate takes questions from the audience.  To leave sufficient time for the closed portion of the exam, the chair has the right to terminate the open session if it goes on beyond one hour.

  2. Closed session.  In this part of the exam, attended only by the student and the committee, committee members ask specific questions related to the dissertation.  Because the committee members have read the entire dissertation, this is their opportunity to ask questions about any part of it, including chapters not presented in detail in the open session.  Once all committee members are satisfied that the questioning is complete, the student is asked to leave the room. The committee then discusses the exam and votes an outcome (see below).  The student is then readmitted and informed of the outcome.  The committee chair sees that necessary forms are signed and returned to the graduate program office.

Dissertation Examination Outcomes

The dissertation exam has three potential outcomes:

  1. Pass.  The student has completed the dissertation requirements for a PhD in biostatistics.  The student then works with the graduate program coordinator to ensure that all other requirements are met prior to deadlines for the proposed graduation date.

  2. Conditional pass.  The defense was satisfactory but additional requirements must be met.  Commonly, the student is asked to address specific questions raised at the defense, or to incorporate edits proposed by committee members.  The dissertation advisor typically oversees these changes, but other committee members may also review changes at their discretion.  Once the additional requirements are met, the student is considered to have completed the dissertation.  The student is not required to defend the dissertation again.

  3. Fail.  The student must defend the dissertation again.

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7.5 Teaching Assistants

7.5.1 Courses That Receive Teaching Assistants

The program assigns TAs to courses in the biostatistics graduate program, the Masters of Science in Clinical Epidemiology, and programs outside of the department such as the Biomedical Graduate Studies program, the Masters of Public Health, or the Masters of Science in Health Policy Research.  The Program Chair assigns TAs to courses based on course needs and student qualifications.

7.5.2 Students Who Serve as Teaching Assistants

All doctoral students are required to spend the equivalent of six hours per week for one semester serving as a TA (1 course unit). Some students serve as full-time TAs during a single half-semester, full semester, or the entire academic year as part of their financial support. In this case the expected workload is 14 to 20 hours per week during the semester. Other students are assigned to serve as part-time TAs or graders, in addition to their RAship, for a lesser number of hours.  Full-time doctoral students may be asked to teach in additional semesters to meet the needs of the department’s educational programs. Students who are fully supported on research assistantships or traineeships are eligible to receive supplementary compensation for additional teaching. Teaching must be completed outside of the hours required for a student’s research assistantship, and must be approved by the Director of Biomedical Graduate Studies.

Benefits and duties of Serving as a Teaching Assistant

In addition to being a degree requirement for all doctoral students, the teaching experience is an opportunity to work closely with a faculty member in the department, review and deepen understanding of the material being taught, and acquire and sharpen teaching skills.

TA duties typically include some or all of the following:

Timeliness in the completion of these duties is essential.  The course instructor and TA should communicate regularly to discuss duties, to share feedback from the students, and to ensure that the TA’s time is being used efficiently.  A student who feels s/he is spending on average more than the designated number of hours on teaching activities should speak to the instructor or, if concerns remain, with the Program Chair.  Both instructors and TAs should recognize that time pressures can vary greatly over the course of a semester. Open communication is the key to a successful teaching experience.

In cases where TA duties include assisting in the grading of exams, course instructors should provide the TA with clear guidance on how to assign points.  Instructors should also recognize that some students may feel awkward evaluating their peers.

TAs should share their e-mail addresses and mailbox locations with their students.  TAs are not on call for their students; nevertheless, students should expect reasonable access to TAs, particularly in the days leading up to exams and project due dates.

TAs are encouraged to speak with the instructor, their academic advisor and the Program Chair about their teaching experiences, particularly if difficulties arise. A potential conflict can often be avoided if its warning signs are recognized early and the situation is handled thoughtfully.

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7.6 Other Policies

7.6.1 Student Travel

BGS allows doctoral students to apply for partial reimbursement (currently, up to $500/year) for travel to professional meetings if they are making a presentation.  Applicants must justify the expenses prior to attending the meetings.  Dissertation advisors sometimes are able to augment these travel funds.  In addition, some training grants provide funds for student travel. See Section 5.6 for further details.

7.6.2 International Students Travelling Abroad

Students are entitled to two weeks of vacation per year.  Unfortunately it is sometimes difficult for international students leaving the US to re-enter in a timely fashion, often due to visa issues.  While the program understands that these issues are largely out of the control of our international students, it also puts a strain on financial sponsors when students are unavailable to carry out the obligations of their research assistantships in person.  International students who leave the country for vacation must make a plan with their sponsor in advance to address the possibility of delayed re-entry.  The written plan must be approved by both the research sponsor and the Program Chair.  Sponsors are not required to allow students to work remotely and, in particular, are not expected to fund students to work remotely for indefinite periods of time.  International students should expect that funding will be suspended if suitable arrangements are not made and/or if students are absent for more than two weeks.

7.6.3 Registration in Biostatistics Courses

Any student who does not have dissertation status and who wishes to take a course in Biostatistics must formally register for the course.  The University reserves the term “auditor” for a student who registers for a course without the intention of receiving a grade and academic credit.  Thus, a non-dissertation student who wishes to “sit in” on a course should register as an auditor in this sense (with permission of the instructor, if required) and pay any applicable tuition and fees.  Requests for waivers of this policy should be submitted to the Chair of the GGEB.

A student with dissertation status (i.e., who is paying dissertation fees and therefore does not pay for course units) may sit in on a course without registering for it.  Students who intend to participate in a course in this way must agree to participate in the course in a manner defined by the instructor, and must obtain the instructor’s prior approval.

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7.7 Committees

Six committees provide governance and administrative leadership to the Biostatistics graduate programs. Membership is subject to change annually.

The Admissions Committee is responsible for the application and admission process.  Responsibilities include developing admission policies; identifying qualified students; reviewing applications; selecting students for telephone or in-person interviews; ranking students for admission; reviewing applications from students in other BGS programs who seek to transfer into Biostatistics; and reviewing applications from students who wish to transfer from part-time (unfunded) to full-time (funded) status in the PhD program.  Admission decisions are subject to approval by the GGEB Executive Committee (a committee of the whole) and the BGS Admission Committee.  The chair of the Admission Committee, together with a designated representative from the Epidemiology PhD program, represents the GGEB in the BGS Admission Committee.

The Curriculum Committee is responsible for all rules and policies related to courses, MS theses and doctoral dissertations.  Responsibilities include developing policies related to course content; reviewing requirements for MS theses and PhD dissertations; approving proposals for the creation of new courses; and reviewing student course evaluations.

The Qualifying Examination Committee conducts the Program’s written qualifications exam. Responsibilities include developing guidelines, policies and procedures for the exam; soliciting questions for the exam; reviewing and selecting questions; creating the exam itself; managing its grading; presenting results to the faculty; and evaluating the merits of appeals of exam results.  Decisions on the outcome of the exam are made by the Biostatistics faculty assembled as a committee of the whole.

The Student Recruitment Committee oversees the recruitment of graduate students into the Biostatistics MS and PhD programs.  Its primary responsibility is to develop and manage student recruitment programs, including the interviewing of candidates selected by the Admission Committee. Members are expected to participate as interviewers.

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8 PhD in Epidemiology Program

8.1 Overview

The mission of the PhD Program in Epidemiology is to train independent researchers in the development and application of epidemiologic methods and to prepare them for positions as scientific leaders in academia and industry. The PhD is a research degree; it indicates the highest attainable level of scholarship, and a commitment to a research career. The PhD does not represent merely the accumulation of course credits, but rather, the development and completion of a well-designed and conscientious program of scientific investigation that makes a unique contribution to the field of epidemiology.

The PhD Program in Epidemiology requires a total of 20 course units including basic and advanced courses in epidemiology, statistical methods, as well as electives drawn from other departments and schools that serve the student’s research interests. The program also requires written qualifications and oral candidacy examinations, and the successful defense of a doctoral dissertation, in accordance with University of Pennsylvania policy. The PhD program typically requires the equivalent of at least four years of full-time study, in three defined phases: coursework, pre-candidacy, and candidacy. The coursework phase typically takes two years of full time study, and is intended to provide the student with the knowledge needed to pursue advanced, independent study and investigation in epidemiologic research. This phase culminates in the written Qualifications Examination, normally taken after most or all of the student’s coursework has been completed. The pre-candidacy phase focuses on the preparation of a scientifically unique, methodologically sound, and feasible dissertation proposal. This phase ends with passing the oral Candidacy Examination, at which time the student is recognized as a Candidate for the PhD and focuses his or her effort on performing the research for and writing the dissertation. A successful public defense of the dissertation then completes the academic requirements for the PhD.

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8.2 Academic advisor

At the time of admission, each incoming student will be assigned an academic advisor who serves as the initial student's primary mentor, advising in course selection and related academic matters. A student may change advisors by request to the Program Chair. A PhD student’s dissertation advisor, once selected, normally assumes the role of academic advisor during the later years of study. At the beginning of the academic year, each student, in collaboration with his/her advisor, prepares a proposed academic program including courses to be taken, courses to be transferred, and timelines for examinations and dissertation preparation.

8.2.1 Policy on advisors

Mentors for students pursuing a PhD in epidemiology will be expected to have extensive training and experience in epidemiologic research.  Generally, they will have a PhD (or equivalent) in epidemiology or related field, OR an MD and Master’s degree in epidemiology or related field, and experience as an independent investigator, as demonstrated through receipt of funding as principal investigator and significant contributions to the epidemiologic literature. Previous experience as a mentor to at least one student in epidemiology at the Master’s level or beyond, including advising through all phases from protocol development to submission of thesis or dissertation, is desirable. Faculty members who do not fulfill all of the criteria may be approved in individual cases by the Graduate Group Chair, in consultation with the Graduate Group Executive Committee. Advisors should expect to dedicate considerable time and effort to one-on-one student supervision.

Mentors not holding the PhD are strongly urged to work closely with the Program Chair and other PhD faculty throughout the student’s program in order to ensure sensitivity to the special and intensive demands of mentoring PhD students.

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8.3 Course requirements

The PhD in Epidemiology typically requires the equivalent of six semesters of coursework plus additional semesters devoted to dissertation research. This can be accomplished in the equivalent of four to five years of full-time study, although depending on the student’s research program, as many as six or even seven years may be needed to complete the program. The current standard course sequence for PhD students consists of nine core courses representing 9.5 course units. A minimum of an additional 10.5 course units are taken in electives (advanced epidemiology and/or biostatistics courses and courses outside the department and school, as needed to serve the student’s specific interests). However, the PhD curriculum is currently under review and these requirements may change; these changes will be reflected in a subsequent version of the Handbook, pending approval by the Graduate Group and Biomedical Graduate Studies. Students are subject to the course requirements in place at the time of admission.

Course descriptions are provided at http://www.med.upenn.edu/ggeb/EpiAcademics.shtml

The core courses required for all PhD students are:

8.3.1 Electives

PhD students are required to take additional elective courses, totaling at least 10.5 course units. At least two of these courses must be advanced courses in statistical applications, such as (but not limited to) EPID 621: Longitudinal and Clustered Data, EPID 622: Applied Regression Models for Categorical Data, EPID 623: Survival Data Analysis, and EPID 680: Causal Inference in Epidemiology. Students meeting additional prerequisites in biostatistics may satisfy this requirement through advanced courses in statistical methods, such as (but not limited to) BSTA 754: Advanced Survival Analysis, BSTA 656: Longitudinal Data Analysis, and BSTA 790: Causal Inference in Biomedical Research.

Elective courses include advanced courses in epidemiology and biostatistics, as well as advanced courses in related disciplines, such as biostatistics, statistics, demographics, sociology, anthropology, economics, and psychology. Students may also arrange to take independent study courses taught by members of the Graduate Group faculty or courses taught elsewhere in the University. However, it is important to select independent study courses carefully, since it is assumed that students will have completed the core at the time of the Qualifications Examination. The student and faculty member will design the activity and the form of the evaluation for the independent study course. Any such proposed independent study course must be approved in advance by the PhD Program Chair. Finally, all electives will be chosen in consultation with the trainee’s faculty advisor.

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8.4 Doctoral seminar

All PhD students are required to participate in the Doctoral Seminar (EPID 700). Advanced students will be expected to present their work and take a leadership role in organizing each session. Students who are in the early stage (coursework phase) of their program will be expected to participate and present selected literature for discussion. The goal of the Doctoral Seminar is to expose all students to a wide variety of epidemiologic research. The seminar meets weekly.

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8.5 Consulting projects

All PhD students must complete a series of consulting projects in epidemiology; this requirement is met by the successful completion of EPID 710. Students normally fulfill this requirement after they have passed the Qualifications Examination, but those with substantial prior experience in epidemiology may, with permission of the Chair, complete the requirement during the first or second year of study. The consulting projects may take one or more forms, such as a one-on-one consultation with an MSCE student or researcher within or outside the department, or formal consultation work in industry. The goal of the course is to demonstrate skill in “on-the-fly” consulting; merely providing database or analytical assistance does not satisfy the requirements for EPID 710. A minimum of three different consulting projects are required for a total of at least 100 hours of consulting work. Students are required to prepare a brief description of each consulting project that includes the name, departments, and titles of those with whom the student is consulting, a paragraph or more on the background of the project, and a detailed description of what the student will do while engaged on the project. This information is provided on the Consulting Project Prospectus Form (Form 6 in Appendix B).  In order to complete the course, the student will submit a report of activities performed for the projects to the EPID 710 course director.

All activities associated with the consulting project(s) must have the approval of the University of Pennsylvania Institutional Review Board (IRB). This requirement is the responsibility of the project principal investigator, if associated with Penn, but students should ensure that they have been added to the pertinent protocol. For consulting projects outside the University, students will need to submit a protocol to the Penn IRB for approval if necessary. No work on any consulting project may begin until Penn IRB approval has been obtained. In addition, the confidentiality of all work and that of individuals associated with the project must be maintained. Project investigators may require a non-disclosure agreement to be signed by the student. The student should review this agreement with his/her advisor prior to signing it, and keep a copy of this agreement for his/her records.

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8.6 Course plans

All students are expected to develop and maintain a current course plan with their advisor. This course plan must be approved by the advisor and the Program Chair and filed with the department’s Office of Graduate Programs. The course plan will be reviewed semi-annually in order to monitor the student’s progress and identify potential delays in completing the program. Typical course plans are shown below.

 

Sample course plan for an entering PhD student

Year
Term
Course
c.u.

 

 

 

 

 

Year 1

Summer II EPID 510:  Introduction to Epidemiology 1.0
  EPID 526:  Biostatistics for Epidemiology I 1.0
 
Fall EPID 542:  Measurements of Health 1.0
  EPID 526/7:  Biostatistics for Epidemiology I (cont’d.)I/II 1.0
  EPID/Other:  Epidemiology or other elective 1.0
  EPID 700:  Doctoral Seminar 0.5
 
Spring EPID 527:  Biostatistics for Epidemiology II (cont’d.) 0
  EPID 532:  Database Management 0.5
  EPID 640:  Advanced Topics in Epidemiology 1.0
  EPID 700:  Doctoral Seminar 0.5
     
Summer I Possible elective 0.5-1.0
     
 

 

 

 

Year 2

Fall EPID/BSTA:  Advanced Biostatistics course or elective 0.5/1.0
  EPID/Other:  Epidemiology or other elective 1.0
  EPID 805:  Applications of Clinical Research 1.0
  EPID 700:  Doctoral Seminar 0.5
     
Spring EPID/BSTA:  Advanced Biostatistics course or elective 0.5/1.0
  EPID 690: Empirical Bioethics 1.0
  EPID/Other:  Epidemiology or other elective 1.0
  EPID 700  Doctoral Seminar 0.5
     
Summer
Qualifications Examination
 

 

 

Year 3

Fall EPID/Other:  Epidemiology or other elective 1.0
  EPID 710:  Consultation in Epidemiology 1.0
  EPID 700: Doctoral Seminar (non-credit) 0
     
Spring EPID/Other:  Epidemiology or other elective 1.0
  EPID 700:  Doctoral Seminar (non-credit) 0
     
Summer
Candidacy Examination
 

 

Year 4

  Dissertation Research 0
  EPID 700:  Doctoral Seminar (non-credit) 0
 
Dissertation Defense

 

Sample course plan for an entering MD-PhD student

Year 1

Fall

Pre-clinical MD curriculum
Indep study (or course if avail)
Spring Pre-clinical MD curriculum Indep study (or course if avail)
Summer   ~8 weeks for ft research
Year 2 Fall

Pre-clinical MD curriculum Case Studies in Translational Research or indep study (or epid course if avail)
Spring Clinical Clerkships  
Summer Clinical Clerkships and Step 1 Typically begin research mid-Aug, slightly before grad semester starts
Year 3 Fall
  4-5 Epidemiology course units
Epi lab rotation, Epidemiology seminar; work on selecting advisor
Spring

4-5 Epidemiology course units; work
Epi lab rotation, Epidemiology seminar

Summer 2-3 Epidemiology course units
Year 4

Fall

Clinical Connections

2-3 Epidemiology course units
Submit F30

Spring   2-3 Epidemiology course units Qualifications examination
Summer   Oral candidacy examination

 

Year 5

Fall

Clinical Connections

Dissertation research

Spring   Dissertation research
Summer   Dissertation research
Year 6 Fall

Clinical Connections

Dissertation research
Spring   Dissertation research
Summer   Dissertation research
Year 7

Fall

Clinical courses (after defending)

 

Spring Clinical courses
Summer Clinical courses
Year 8

Fall

Clinical courses; boards 2

Clinical courses; Dean's letter OCT 1

 

 

Spring

Residency interviews (~Nov-Jan)
Clinical courses and/or research
GRADUATION

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8.7 PhD Examinations

In addition to course-specific examinations, there are three PhD examinations required in order to ensure rigorous, appropriate evaluations during the phases of a student’s program. These examinations are described below.

  1. Written Qualifications Examination

a. The Qualifications Examination will be taken after the equivalent of two years of course work.

b. The Qualifications Examination will be open-book and consist of three parts, administered over a one-week period:

i. General epidemiology

1. A series of questions and problems to assess competency in basic and advanced epidemiologic concepts, critical appraisal, and measurement

ii. Research methods  

1. A series of questions and problems to assess competency in biostatistical and quantitative and qualitative epidemiologic methods.

iii. The student’s content area of interest (e.g., genetic epidemiology, pharmacoepidemiology) and/or biostatistics minor

1. This section will evaluate the student’s ability to integrate biological and clinical principles with epidemiologic knowledge and skills by writing a short grant proposal that addresses a research question provided by the committee. The proposal will include Specific Aims, Background and Significance, and Research Plan, and be limited to no more than 10 pages, not including references.

c. Questions for the qualifications examination will be written and graded by the PhD Program Examination Committee.

i. Questions for the general epidemiology and methods section will be written and graded by the committee.

ii. Questions for the area of interest section will be written and graded by either members of the committee with expertise in the student’s area, or by faculty added to the committee as ad hoc members for this purpose.

d. Students must pass all three parts of the Qualifications Examination in order to advance to the next phase of the PhD program. Those who fail one or more parts of the examination may re-take those parts once, but a passing grade on all three parts must be attained before the end of the second year of study. Given the highly subjective nature of the grant proposal component of the examination, the student automatically qualifies for one oral rebuttal and retake in the case of a failing grade on this component.

e. Transfers from the MSCE program must take the PhD Qualifications Examination, even if the MSCE comprehensive examination was taken previously.

f. Grandfathering: MSCE students who have transferred to the PhD program before January 1, 2009 are exempt from this policy. These students will have taken the MSCE comprehensive examination as their qualifications exam, and will be required to take another written examination, comparable in difficulty to the PhD qualifications exam and in addition to the oral exam, prior to being admitted to candidacy status, as has been done historically in the PhD program.

g. Review of the examination

i. A student may request to review his exam paper in company with the Examination Committee Chair. The purpose of such a review is to help the student evaluate the types of mistakes made, identify areas where further study is needed, etc. The Examination Committee retains the graded exam papers and does not return them to the students.

h. Appeal process

i. A student may appeal the outcome of the Qualifications Examination to the Examination Committee Chair, who together with the full committee will evaluate the appeal and judge whether it has merit. A grade can only be changed in cases of a specific error in scoring. The Examination Committee refers any grade change that could affect the student’s exam outcome to the full GGEB Executive Committee, who decides whether to revise the exam outcome.

ii. Because a minor revision of the score is unlikely to change the exam outcome, a student should only initiate a formal appeal if there were one or more egregious errors in the problem or in its grading, the correction of which would likely lead to a substantial increase in the score. A student who seeks a formal review must request it, in writing, from the Examination Committee Chair within one week of the issuance of the letter notifying the student of the exam result.

2. Candidacy Examination

a. The Candidacy Examination must be passed within 18 months of the Qualifications Examination.

b. The Candidacy Examination is administered by the Dissertation Committee (see Section 8.8.2).

c. The focus of the Candidacy Examination is on the student’s proposed dissertation research, but other material may be included as desired by the student’s committee.

d. The Candidacy Examination will consist of two parts:

i. Written: dissertation proposal, submitted to the student’s committee at least one month prior to oral proposal defense, and approved by the committee prior to the oral proposal defense

ii. Oral: Oral defense of proposal (non-public) before the committee with the inclusion of additional pertinent material at the discretion of committee

e. Students must pass both parts of the Candidacy Examination in order to advance to the final phase of the PhD program. Those who fail the Candidacy Examination may re-take it once, at the discretion of the committee.

3. Dissertation Defense       

a. The final oral examination is the Dissertation Defense. The defense must be announced by public advertisement at least four weeks in advance using such venues as the GGEB website, posted announcements in Penn Medicine spaces (as allowed), and electronic mail.

b. The defense should be scheduled when the candidate and the dissertation advisor agree that the research is near completion and the draft dissertation is in a format suitable for distribution to the committee. As soon as a date and time are fixed, the graduate program staff reserves a room (for at least two hours) and prepares the necessary public announcements.

c. All dissertation committee members should be present for the final defense. In emergencies, one member may participate in the defense by telephone.  That member cannot be the committee chair, the student’s advisor, or the biostatistics faculty (if there is only one biostatics faculty member on the committee). If one or more committee members are absent (i.e., not present or not participating by telephone) from the final defense, it cannot proceed and must be rescheduled.

d. Format of the defense

i. At least two weeks prior to the exam, the student should provide each committee member with a copy of the full dissertation. The committee members review the dissertation and prepare exam questions based on it.

The defense consists of two parts:

1. Open session. The chair describes the process to all attendees and introduces the candidate. The candidate then presents his/her research in the style of a departmental colloquium. Typically, the candidate presents one chapter in depth, with a very brief overview of the others. This presentation should not exceed 45 minutes. At the close of the formal presentation the candidate takes questions from the audience. The chair has the right to terminate the open session if it goes beyond one hour.

2. Closed session. In this part of the examination, attended only by the student and members of the committee, the student is asked specific questions pertaining to the dissertation. Because the committee members have read the entire dissertation, this is their opportunity to ask any questions about any part of it, including material not presented in the open session. Once the committee members are satisfied that the questioning is complete, the student is asked to leave the room and the committee deliberates in closed session. During this time, the committee reviews the student’s work, draws up a list of recommendations, and votes an outcome. The student is then readmitted to the room, informed of the outcome, and is provided with any recommendations. The committee chair sees that necessary forms are signed and returned to the graduate program office.

ii. The defense will be coordinated by the dissertation committee chair. This individual will be responsible for maintaining order and the sequence and timely completion of the examination.

e. The dissertation exam has three potential outcomes:

i. Pass. The student has completed the dissertation requirements for a PhD in epidemiology. The student then works with the graduate program staff to ensure that all other requirements are met prior to deadlines for the proposed graduation date.

 ii. Conditional pass. The defense was satisfactory but additional requirements, usually minor, must be satisfied. Commonly, the student is asked to address specific questions raised at the defense, or to incorporate edits proposed by committee members. The dissertation advisor typically oversees these changes, but other committee members may also review changes at their discretion. Once the additional requirements are met, the student is considered to have completed the dissertation. The student is not required to defend the dissertation again.

iii. Fail. The student must defend the dissertation again; only one additional attempt at the final defense is allowed.

f. Dissertation acceptances must be unanimous, in writing, and signed by all members of the dissertation committee. Approved dissertations must be submitted to the Graduate Council of the Faculties in a format that meets the style standards established by the Vice Provost for Graduate Education.

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8.8 Preparing the dissertation

8.8.1 Dissertation advisor

PhD in Epidemiology students must carry out their dissertation research under the mentorship of a faculty member of the GGEB. The dissertation advisor is the most important individual the student will interact with in the course of their graduate training. For this reason students should carefully evaluate their interests and experiences in choosing the advisor. The student’s dissertation advisor may not be the Dissertation Committee chair, but may be (and is usually) the student’s academic advisor.  See Section 5.2.1.for information about advisor qualifications.

8.8.2 Dissertation committee

Each student will organize a Dissertation Committee according to the following constituency. The committee will consist of at least four members, the majority of whom will be members of the GGEB. A GGEB faculty member will be appointed as the Chair of the committee by the student’s advisor. The role of the Chair is to run committee meetings and to oversee the candidacy examination and final defense.  At least one member of the Dissertation Committee must be a member of the faculty in the Division of Epidemiology and ordinarily at least one other should be a member of the faculty in the Division of Biostatistics of the Department of Biostatistics and Epidemiology. These committee members will be collectively responsible for administering and evaluating the oral Candidacy Examination, reading the dissertation, and evaluating the final defense.  Additional content experts from within or outside the GGEB may be added to the committee as needed. The initial constituency and any changes in the membership must be approved by the Program Chair and the Graduate Group Chair. This Committee will be in place at all times during the dissertation phase. If for some reason, a student changes to a different area of research, a new Dissertation Committee must be appointed immediately and must meet within three months to discuss new plans for the dissertation research.

8.8.3 Additional biostatistics support

The biostatistics faculty member(s) on the Dissertation Committee will provide advice and collaborate on the scientific design and statistical analyses required for the dissertation research, but it is the student’s responsibility to perform such analyses. If appropriate, it may be possible to substitute the GGEB biostatistics faculty member with biostatistics faculty from another department at Penn or from outside the University, upon approval by the Program Chair and the GGEB Chair. If a student’s dissertation research area requires additional statistical expertise, appropriate biostatistics faculty should formally be added to the Dissertation Committee.

8.8.4 Computing, programming, and database support

The student is responsible for writing all parts of the dissertation, including any methodological sections, and for conducting or directing all analyses; this ordinarily includes obtaining, preparing, and maintaining data needed for the research. Depending on the student's research program, additional (non-faculty) assistance with computing, programming, and database development may be requested by the student. However, to ensure that the student gains the maximum possible experience with these critically important skills, this request must be approved by the dissertation advisor and the Program Chair. Upon approval, the student should make arrangements with the Biostatistics Analysis Center (BAC), the Clinical Research Computing Unit (CRCU), or other computing group or consultant as needed. The student and dissertation advisor are responsible for obtaining the necessary funding to defray non-faculty support costs.

8.8.5 Frequency of dissertation committee meetings

Once a student has advanced to candidacy, his/her Dissertation Committee will review goals and progress twice each year. The committee chair should complete the Dissertation Committee Meeting Report form and submit this to the Program Chair within 15 days of each committee meeting.

8.8.6 Laboratory notebook

BGS mandates that the student’s Dissertation Committee, at each of its meetings, review the student’s “lab notebook”. The PhD Program in Epidemiology interprets this to mean that the student should make available for faculty review, upon request, primary documentation of any substantial element of the dissertation. Such a review takes place at the Candidacy Exam and any subsequent meetings of the committee prior to, but not including, the dissertation defense. Examples of materials subject to review include the statement and investigation of a research question; the code and results of a simulation study; or the data, code and results of a data analysis. Prior to the meeting, the student’s advisor, in consultation with the Dissertation Committee, designates a short list of such items that the student makes available in electronic or hard-copy format. The committee chair sets aside time at the meeting for the review of this material. In keeping with the BGS policy, there is no expectation that the committee should scrutinize all such documents “in their entirety”; rather, the review should be sufficient to satisfy the committee that the student’s research records are “complete and well managed”.

8.8.7 Content and format of the dissertation

The dissertation must be a scholarly work, providing a written account of an independent investigation of an epidemiologic question or series of related epidemiologic questions. It will be in the form of a monograph, containing one or more research questions about the epidemiology of a particular health topic or disease. Within this monograph, there will be at least three separate manuscripts of publishable quality, one of which must offer a novel methodologic approach to a question in epidemiologic research. It will include the formulation of one or more hypotheses, a review of the appropriate literature, a description of the project, data collection, data analysis, data interpretation, discussion of the findings, and limitations of the work. If the dissertation involves the investigation of more than one question, each question must focus on an epidemiologic or methodologic issue related to the health topic or disease under investigation. The dissertation project should demonstrate that the candidate has a command of the subject and a thorough knowledge of the research methodology used to investigate the question(s).

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8.9 Non-credit requirements

8.9.1 Teaching practicum

Students in the PhD program must spend one semester providing teaching support as a Teaching Assistant (TA) for an Epidemiology or Biostatistics course. In addition to being a degree requirement for all doctoral students, the teaching experience is an opportunity to work closely with a faculty member, to review and deepen understanding of the material being taught, and to acquire and sharpen teaching skills. TAs are usually assigned to core courses in the Master of Science in Clinical Epidemiology program, but students may find teaching in one of the elective courses, or other epidemiology-related courses in other departments to be of interest as well. The Program Chair assigns TAs to courses based on course needs and student qualifications, in consultation with the course director, the student, and his/her advisor. Upon assignment, students must prepare a teaching assistance plan in writing, signed off by the course director and approved by the chair, for TA activities related to the course. This plan must be completed at least four weeks prior to the start of the course. The form for this plan is found in Appendix B (Form 5).

TA duties typically include some or all of the following:

Please note that merely serving as a grader in a course does not fulfill the TA requirement for the doctoral program. The student must make a substantive contribution to the course.

Timeliness in the completion of these duties is essential. The course instructor(s) and TA should communicate regularly to discuss duties, to share feedback from the students, and to ensure that the TA’s time is being used efficiently.

Both instructors and TAs should recognize that time pressures can vary greatly over the course of a semester. For instance, TA duties usually are light at the start of the course, heavy in the middle, and then light again toward the end (unless assistance is required grading exams).

Experience shows that grading homework and preparing and directing lab or discussion sessions are the two items that occupy most of a TA’s time, especially for first-time TAs. TAs should not hesitate to request specific direction on what to present in lab or discussion sessions. Although the success of a course is ultimately the instructor’s responsibility, students should recognize that instructors cannot be expected to solve problems that they don’t know exist. Open communication is the key to a successful teaching experience. In cases where TA duties include assisting in the grading of exams, course instructors should provide the TA with clear guidance on how to assign points. Instructors should also recognize that some students may feel awkward evaluating their peers.

The course director may provide the opportunity for the TA to prepare and deliver at least one lecture. In this case, the course director should allow the TA sufficient time to prepare the lecture and should offer any necessary guidance about what is to be covered. Whenever possible, the TA’s lecture will be videotaped and reviewed with the course director and his/her mentor in order to identify strengths and weaknesses.

To ease communication, TAs should share their e-mail addresses and mailbox locations with their students. TAs are not on call for their students; nevertheless, students should expect reasonable access to TAs, particularly in the days leading up to exams and project due dates.

8.9.2 Weekly seminar

A fundamental component of the PhD program is attendance at the weekly Center for Clinical Epidemiology & Biostatistics Seminar, at which faculty and researchers within and outside of Penn present their work or discuss timely issues in epidemiology. All PhD students are required to attend this seminar series weekly, unless excused due to scheduling conflicts, illness, or other reason. Excuses should be made with the Academic Coordinator, either before or as soon as possible after a missed seminar. Advanced PhD students are also welcome to present at this seminar. However, slots fill up early in the academic year, so it is best to discuss any plans to present with the advisor and the Chair of the Seminar Committee. Students are also encouraged to suggest experts from the field as potential seminar speakers to the Seminar Committee.

8.9.3 Research rotations

In order to provide doctoral students with as much exposure as possible to a broad range of research activities and opportunities during their first year of study, they are required to engage in project rotations with GGEB faculty. The following procedures define the rules for engaging in these rotations.

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8.10 General program policies

8.10.1 Exemptions and modifications

Trainees may place out of the following courses only, upon passing an examination administered by the course instructor: Introductory Epidemiology, Introductory Biostatistics, and Database Management for Clinical Epidemiology. Electives should be taken so that the total number of course units still equals 20. The student should justify the request to place out of a course, and the request should be accompanied by reprints, abstracts from meetings, course syllabus, or other appropriate material. Such requests are made in writing as a letter to the Academic Review Committee and should be made before the end of the first semester in the program.

8.10.2 Terminal master's degree

The PhD Program in Epidemiology does not admit students for study towards a Master's degree.

8.10.3 Student memberships

All PhD students in Epidemiology are encouraged to join one or more professional societies, but especially the American College of Epidemiology as an Associate or the Society for Epidemiologic Research as a Student Member.

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8.11 Facilities

8.11.1 Program web-resource

The PhD Program will use Canvas to provide student-related forms, resources and web links. These pages can be accessed by logging in to https://canvas.upenn.edu/

8.11.2 Student Space

The PhD program has space for students on the first floor of Blockley Hall. It includes a group meeting room equipped with two conference tables, whiteboards, and computer projection capability; a room with 30 study carrels; and lockers. There is also wireless connectivity throughout the first floor of Blockley Hall. Administration of the carrels and locker assignments is managed through the Office of Graduate Training (918 Blockley Hall).