The primary goal of the training program offered by the Neuroscience Graduate Group (NGG) is to develop first-rate scientists who excel in neuroscience research. The NGG program offers a PhD degree either alone or as part of a Combined Degree (CD) in tandem with either an MD or VMD degree.

The NGG does not have a Master of Science (MS) program and does not admit students who wish to obtain an MS degree. MS degrees are not ordinarily awarded at an intermediary point in the program. However, if a student leaves the program for compelling personal reasons or is asked to leave the program, the Academic Review Committee (ARC) may consider awarding a terminal MS degree, but only if the student: i) has completed two years of coursework and laboratory rotations, ii) is in good academic standing, and iii) has passed the Candidacy Exam


1.1. General requirements
1.2. Advising
. . . . 1.2.1. Individual Development Plans (IDPs)
1.3. Financial support
. . . . 1.3.1. Institutional training grants
. . . . 1.3.2. Individual fellowships
. . . . 1.3.3. Annual dues for society membership
. . . . 1.3.4. Travel to professional meetings
. . . . 1.3.5. Specialty courses
. . . . 1.3.6. NIH reporting requirements
1.4. Program activities
 . . . 1.4.1. Seminars
 . . . 1.4.2. Retreats and other special events
. . . . 1.4.3. Student-led activities
1.5. Outreach
1.6. Teaching assistantships
1.7. Responsible Conduct of Research (RCR)/Scientific Rigor and Responsibility (SRR)
 . . . 1.7.1 RCR/SRR training
 . . . 1.7.2 Laboratory notebooks
 . . . 1.7.3 Academic integrity
 . . . 1.7.4 Use of Artificial Intelligence (e.g., ChatGPT)
1.8. Leave of absence
1.9. Mail
1.10 Letters of recommendation

1.1. General requirements 

Before taking the Candidacy Exam, students are required to take Core and elective classes and participate in laboratory rotations, journal clubsretreats, and other programmatic activities. PhD candidates complete these requirements in their first two years in the program. CD candidates enter the NGG with one year of advanced academic standing because of their medical or veterinary training and thus complete these requirements in their first year in the program. At the end of this period, students must successfully complete the Candidacy Exam.

After the Candidacy Exam, students continue to participate in journal clubsretreats, and other programmatic activities. They also are required to serve as Teaching Assistants for one semester, which typically takes place during the year following the Candidacy Exam. Otherwise, students devote themselves to research on a problem whose solution will constitute a significant advance to some area of neuroscience. The PhD in Neuroscience is awarded when the resulting Thesis is successfully defended before the faculty.

The NGG training program is designed to be flexible. Therefore, students are encouraged to discuss the existing requirements and/or suggest possible customizations with their mentor(s), the Academic Review Committee, and/or the NGG Chair.

Section updated on 12/03/2023.

1.2. Advising

Each NGG student receives advising from multiple sources:

The Academic Review Committee (ARC) provides advising to all students prior to the Candidacy Exam. The ARC meets two times per year, around the beginning of the Fall and Spring semesters. The purpose of the ARC is to review each student’s performance and address any concerns from the previous semester and to help finalize plans for the upcoming semester.

The ARC consists of both faculty and senior student representatives from the NGG. The Committee is divided into multiple advisory subgroups, each consisting of several (typically 2-4) faculty and one student representative. Each subgroup advises an assigned subset of incoming students from the Fall semester of their first year until their Candidacy Exam Committees are formed (Spring semester of year 2 for PhD students, year 1 for CD students). Each advisee is assigned a primary mentor from the three faculty on the advisory subgroup to serve as a consistent point of contact during this time. The current membership roster is listed here.

The meetings scheduled around the beginning of September (for the fall semester) and December (for the spring semester) include ~15-min sessions with each student and the appropriate advisory subgroup. Students should come to these meetings with a carefully considered plan for course and laboratory work. These meetings are organized as follows. First, the ARC student representative leaves the room so the advisee's academic file and other potentially sensitive issues can be discussed. Next, the student representative returns to the room and the full subgroup discusses with the advisee plans for course and laboratory work in the upcoming semester. The subgroups are designed to include members with a wide range of experience and expertise. Nevertheless, on occasion, questions about a proposed course or rotation may arise that cannot be answered effectively by the subgroup; in these cases, the issues will be discussed by the full ARC and then reported back to the student by a representative of the advisory subgroup. Finally, the primary advisor, with the advisee's input, fills out the ARC Meeting Form to be returned to the NGG Coordinator. It is understood that not all course and rotation decisions will be finalized at this meeting. Students have an additional 7–10 days to finalize their schedule and inform the NGG Coordinator, who registers students for all courses.

The ARC also reviews the Candidacy Exam performance of all NGG students and is available to consult on any other academic-related issues for dissertation-level students.

The Candidacy Exam Committee can provide advising in the months leading up until and including the Candidacy Exam, and in the subsequent few months while the student is forming a Thesis Committee.

The Thesis Advisor provides advising from the time the student enters the advisor's laboratory, through the Candidacy Exam, and up to and including the Thesis Defense.

The Thesis Committee provides advising throughout the Thesis years, up to and including the Thesis Defense.

The NGG Chair and the Vice Chair (Director of Advising) are available to provide advising and guidance to all NGG students at all points in their graduate careers.

All students and faculty should be familiar with University policies and guidance on advising and mentoring.

Section updated on 12/03/2023.

1.2.1. Individual Development Plans (IDPs)

BGS requires an annual IDP for all predoctoral (PhD and CD) students to help ensure that they are effectively working towards their career goals. 

Years 1 and 2 PhD students and Year 1 CD students use the "BGS Predoctoral Student IDP – for Junior Students.” Students are required to bring a filled-out copy of part B of the form to the September ARC meeting (both years for PhD students, just year 1 for CD students), which will be saved in the student's academic file. Students should update the IDP, as needed, for the December ARC meeting. Students will discuss the IDP with the ARC. Students are also encouraged to discuss the IDP with their Rotation Advisors and Thesis Advisors once they are selected.

Post-CE students use the "BGS Predoctoral Student IDP – for Students in Thesis Labs.” Students are required to fill out parts B and C of the form and provide a copy to the NGG Coordinator at least once per academic year. The student’s Thesis Committee will check at each meeting whether or not this was done and discuss the IDP with the student. Students are encouraged to discuss the IDP one-on-one with their Thesis Advisor.

Section updated on 12/03/2023.

1.3. Financial support

Students accepted into the program will be provided with a stipend, plus tuition, fees, and health insurance coverage. In return, the NGG expects full-time effort, and thus, with the exception of certain teaching activities, students may not engage in outside employment. In exceptional circumstances, such outside employment may be in the educational interests of the student. If so, the student should apply in writing to the NGG Chair for permission to take such employment.

The Biomedical Graduate Studies (BGS) Program, in concert with the NGG, provides financial support for students until June 1 of year 2 (PhD students) or September 1 of graduate year 2 (CD students). The Thesis Advisor assumes substantial financial responsibility thereafter.

Students must inform the NGG Chair as soon as they have identified their thesis lab. The NGG Chair and BGS Financial Director will then ensure that the advisor has in place the needed financial support. If such support is not available, then the student will have to select another lab in which to pursue their thesis work.

Section updated on 12/03/2023.

1.3.1. Institutional training grants

Penn typically has a number of institutional training grants sponsored by either the NIH or NSF that can support NGG students. One, the Neuroscience Training Grant, supports a number of NGG students in their first two years, prior to taking the Candidacy Exam. All other training grants support students in their Thesis years. Typically these training grants will cover a portion of the student’s stipend and tuition (the PI is responsible for the rest) for up to two years, as long as the student meets eligibility requirements (e.g., citizenship) and is working on a project that is relevant to the training program. In some cases, these training grants will also provide the student with some additional funds for equipment and/or travel.

See the BGS website for a list of active, neuroscience-related training grants and PI contact information.

Section updated on 12/03/2023.

1.3.2. Individual fellowships

Prior to the Candidacy Exam, each first-year PhD student is required to apply for at least one individual pre-doctoral fellowships from an outside source. CD students are encouraged, but not required, to do so. Learning how to apply for outside funding is an important part of graduate training, and receipt of such a fellowship is a prestigious addition to one’s CV. The most commonly targeted fellowship for pre-Candidacy Exam students is the National Science Foundation (NSF) Graduate Research Fellowship. CD students are not eligible for this fellowship. Eligible NGG students have also applied for other fellowships including The Paul & Daisy Soros Fellowships for New Americans, the Howard Hughes Medical Institute International Student Research Fellowships, the Department of Energy Computational Science Graduate Fellowship, the National Defense Science & Engineering Graduate Fellowship (NDSEG), and the Ford Foundation Predoctoral Fellowship.

BGS maintains a list of individual fellowship opportunities across many biomedical-related disciplines that can be found on this page

The NGG Chair helps students to identify appropriate fellowships and faculty sponsors. The NGG Chair also holds a workshop in the Fall semester to describe the application process and can help provide guidance on preparing the proposed training and research program. Most commonly, the research proposal for these fellowship applications is developed from previous or ongoing lab rotation projects.

Schedule for NSF applications for Fall 2023:
September 21, 2023  1-2:30 PM: NGG Information Session

Deadlines (all applications/reference letters are due by 5pm EST):
October 16: Application due for Life Sciences
October 17: Applications due for Social Sciences and Psychology
October 27: Letters of Recommendation due

Please see here for more information about the NSF deadlines.

See the NSF GRFP website for more details. View successful applications from NGG students and alumni on the NGG Canvas page.

Upon successful completion of the Candidacy Exam, eligible students are required to apply for support via an Individual Predoctoral NRSA fellowship from the NIH (PA-21-051 or PA-21-052). Only citizens or permanent residents of the United States are eligible. Students who have already been awarded outside fellowships are exempted. NGG students have often been successful at obtaining these fellowships, with an over 50% success rate since 2006. To apply:

  • Well in advance of the application deadline, communicate with the BGS Finance Office (Grants Manager: Marianne Altland Williams) to learn about the submission process, which is done through that office. 
  • Prepare the application in collaboration with your Thesis Advisor. Writing the scientific portion of the application is typically straightforward because it has the same form and content as the written portion of the Candidacy Exam.
For more information consult the Canvas site for NRSA and other grant submissions.

Section updated on 12/03/2023.

1.3.3. Annual dues for society membership

All NGG students are encouraged to apply for membership in the Society for Neuroscience, the broadest professional organization in our field. There are many benefits of membership, including receipt of SfN's Neuroscience Nexus newsletter, discounts on attending the Annual SfN Meeting and Journal of Neuroscience subscriptions, and, importantly, only SfN members can be the first author or sponsor of abstracts for the Annual SfN Meeting.

To join the SfN as a Student Member, students need two faculty sponsors. One of the two can come from the NGG Chair. Please e-mail the NGG Coordinator with “SfN Student Membership” in the subject line to have her send you a sponsoring e-mail from the NGG Chair. You can ask your rotation advisor or any other NGG faculty member who is also a SfN member to write the other sponsor email.

Some students will instead opt to join a different professional society, for example those that host other annual meetings with neuroscience-related themes.

The Mahoney Institute will reimburse all students for the cost of student membership in a professional society (assuming the costs are roughly on par with a student membership to the SfN). If you are applying for SfN (or other) membership for the first time, you will be reimbursed using your proof of payment, such as a credit card receipt. Submit your request for reimbursement through Penn's Concur system. The system will ask for the name of the person who approves the expense, so please use John Westdyke's name. Access the Concur system here.

Students who are renewing their membership should contact the Neuroscience Department Business Office at 215-898-8754.

Please note that reimbursement for membership dues is completely separate from getting reimbursed for travel expenses for attending a professional meeting, described below.

Section updated on 12/03/2023.

1.3.4. Travel to professional meetings

Students who are presenting work at a meeting can apply for travel funds, using the on-line BGS travel request form found hereYou must submit your request at least 21 days before the conference start date or it will not be considered by BGS. BGS provides $1000 for each student to present work at one meeting each year; see the BGS travel page ("Travel Funds" entry) for details.

In many cases, additional funds will be needed to cover all expenses. These funds typically come from one or more of the following sources. Be sure to confirm the availability of these funds before filling out the BGS travel request form, which must include all other sources of funding and the amount covered by each source. These sources include:

  • Pre Candidacy Exam students supported by the Neuroscience Training Grant can receive up to $300 from that training grant, regardless of whether or not they are presenting their work at the meeting. E-mail the PI (Minghong Ma) with this request.
  • Post Candidacy Exam students supported by other training grants or individual fellowships often have funds available for travel. Contact the training grant PI or the BGS Financial Director for more information.
  • Students who are presenting their work at a professional meeting are eligible to apply for the Jameson-Hurvich Travel Award (for any meeting where the student is presenting work related to behavioral neuroscience). An announcement goes out around the beginning of the Fall and Spring semesters. The NGG Awards Committee selects several recipients, who are announced around the beginning of the Fall and Spring Semesters.
  • The BGS travel page (see "Travel Funds" entry) lists other travel grant mechanisms available to BGS students.
  • Any remaining funds are typically covered by the faculty member who sponsored the research; i.e., the Thesis Advisor for thesis-level students or the Rotation Advisor for pre Candidacy Exam students.

Students who are not requesting BGS funds do not need to submit a request for travel. Reimbursements are submitted in Concur. In the "Comment to Approver" mention how travel is being funded (ex: training grant, name of mentor).

Section updated on 12/03/2023.

1.3.5. Specialty courses

Each year, several neuroscience-related specialty courses that might be of interest to NGG students are offered by various organizations, including the Marine Biological Laboratory (MBL) in Woods Hole, MA, and the Cold Spring Harbor Laboratories in Cold Spring Harbor, NY. These courses are typically most appropriate for Thesis-level students, who must obtain permission from their Thesis Advisor before applying.

BGS will contribute up to $1,500 for BGS students toward the cost of attending one of these outside specialty courses, with some restrictions; see the BGS travel page ("Travel Funds" entry) for details. The Thesis Advisor must cover any remaining balance.

Section updated on 12/03/2023.

1.3.6.NIH reporting requirements

NIH-sponsored individual fellowships, training grants, and other sources of financial support require annual progress reports, among other administrative duties. These reports typically include appropriately formatted NIH biosketches (always check the NIH website for the latest instructions). One common mistake in preparing these biosketches is omitting or improperly using PMCID (PubMed Central ID) numbers, which are required for all listings of manuscripts published since 2008. The PMCID refers to the manuscript identifier in PubMed Central, the free digital archive of full-text biomedical and life sciences journal literature at the NIH. Do not confuse these numbers (which begin with "PMC") with the PMID (PubMed ID) numbers, which are associated with PubMed citations and not the full-text articles in PubMed Central.

Here is a useful tool for converting PMIDs to PMCIDs.

Here is a FAQ for the NIH public access policy.

Non-NIH sources of funding also have their own reporting requirements. Be sure to check with the sponsoring agency for details.

Section updated on 12/03/2023.

1.4. Program activities

1.4.1. Seminars

There are many seminars covering various areas of Neuroscience that occur as parts of several programs on campus. All upcoming Neuroscience-related seminars on the Penn campus are listed on the MINS website and are sent to all NGG students and faculty in an e-mail each Monday.

A major venue for weekly Neuroscience seminars is the series sponsored by the MINS, in concert with the Neuroscience Training Grant. This seminar series covers a wide range of topics in Neuroscience. The seminars are given on Wednesdays at 4:00 p.m. in the John Morgan Class of 1962 Auditorium. All pre-Candidacy Exam students are required to attend, and all Thesis-level students are strongly encouraged to attend. Students are invited to lunch with seminar speakers preceding their talks.

Section updated on 12/03/2023.

1.4.2. Retreats and other special events

All students are expected to participate in the following important gatherings of our local Neuroscience community:

  • The Louis B. Flexner lecture and dinner plus the Behavioral Neurosciences Training Grant Retreat, both of which are held during the Fall Semester.
  • The Annual MINS Retreat, which is typically held in April.
  • The NTG/OTO/Vision Sciences Training Grants Retreat, which is typically held in May/June.

Other special events may also be held given available resources. 

Section updated on 12/03/2023.

1.4.3. Student-led activities

Student-led activities are organized by the Graduate-Led Initiatives and Activities (GLIA) Committee. These activities can include workshops, student-faculty lunches, and a student-led retreat. Oversight is provided by the NGG Coordinator, Vice Chair, and Chair.

Interested students should contact GLIA directly.

Section updated on 12/03/2023.

1.5. Outreach

The NGG is active in community outreach and partnership activities in the Philadelphia area. Participation by NGG students is not required but encouraged. Regular events include the Kids Judge! Neuroscience Fair for elementary school children, the Regional Brain Bee for high school students, and the Upward Bound Neuroscience Course for high school sophomores and juniors.

Students interested in participating should contact GLIA or the NGG Coordinator or Chair.

Section updated on 12/03/2023.

1.6. Teaching requirement and opportunities

All students are required to serve as Teaching Assistants for one semester in one of several courses in Penn’s undergraduate Neuroscience (formerly Biological Basis of Behavior, or BBB) program, including Introduction to Brains & Behavior (NRSC 1110, Fall and Spring Semesters) and Cellular Neurobiology (NRSC 2110, Fall Semester). These TA-ships provide NGG students with important teaching experience and help to better integrate the primary graduate and undergraduate neuroscience programs on campus. They typically occur in the year immediately following successful completion of the Candidacy Exam. The NGG Chair makes the TA assignments during June or July for the coming academic year. Efforts will be made to place students in courses of their choice, but each course must be covered fully and thus occasionally options are limited. 

In the rare cases in which the NGG student fails to make the expected contribution to the TA-ship, as defined by the course instructor and reviewed by the NGG and ARC Chairs, the student will be required to repeat the TA-ship in a subsequent semester. The repeat TA-ship also includes an NGG contribution to the student's normal stipend but no additional remuneration.

In addition to the one-semester TA requirement, students are allowed to pursue two other paid teaching opportunities, according to BGS rules. Students interested in pursuing a career in teaching should pay particular attention to this limitation because they need to make the most of each teaching opportunity. Each additional teaching opportunity requires an approval letter from the student’s Thesis Advisor (for post-Candidacy-Exam students) to the NGG Chair, or direct approval from the NGG Chair (for pre-Candidacy-Exam students), and include:

  • Individual tutoring for first-year NGG students taking Core II or BIOM 6000. Second-year (i.e., pre-Candidacy-Exam) students who performed well in these courses are often recruited because of their recent exposure to the material. Whether or not this activity counts towards the BGS-mandated maximum of two additional paid teaching experiences is determined on a case-by-case basis, typically by considering the weekly commitment. 
  • Sometimes other undergraduate Neuroscience courses or other courses at Penn request additional TAs from the NGG (these requests must be approved by the NGG Chair). Only students who have already fulfilled their one-semester TA requirement will be considered for these positions. Participating students will be remunerated at the rate of $5,500 for a regular TA, or $6,500 for a head TA, per semester of TAing, in addition to their regular stipends.
  • Several of our students have participated in workshops sponsored by Penn’s Center for Teaching and Learning (CTL) that train experienced TAs to help train new TAs. Because students who participate in these workshops receive a stipend, they are counted towards the BGS-mandated maximum of two additional paid teaching experiences.

Any additional paid teaching opportunity (e.g., serving as a TA Trainer for the Center for Teaching and Learning) must not be a substantial time commitment and requires official permission from the student's advisor, NGG, and BGS.

More information on TA responsibilities, including details about specific courses, can be found on the NGG Canvas site.

Section updated on 12/03/2023.

1.7. Responsible Conduct of Research (RCR) and Scientific Rigor and Responsibility (SRR)

All NGG students must be aware of and follow all relevant policies concerning conduct, academic integrity, and other expectations of graduate students here at Penn. BGS policies can be found here. University policies can be found here

Section updated on 12/03/2023.

1.7.1. RCR/SRR training

In accordance with NIH regulations, all BGS students receive formal training in the Responsible Conduct of Research and Scientific Rigor and Responsibility every year. Topics include: Research Misconduct; Data Acquisition, Management, Sharing and Ownership; Mentoring; Collaboration; Conflicts of Interest; Publication Practices, Responsible Authorship and Peer Review; Human Subjects and Animal Welfare. Training consists of on-line courses and quizzes, small-group workshops, courses, seminars, and symposia.

Section updated on 12/03/2023.

1.7.2. Laboratory notebooks

All NGG students must maintain appropriate laboratory notebooks for all research activities in both their laboratory rotations and their thesis work. Students are required to bring to each Thesis Committee meeting all of their laboratory notebooks that they used since the previous meeting.

Laboratory notebooks are records of all activities that are relevant to the collection and storage of data in an experiment. Notebooks can take many different forms, including written and electronic. In both cases, care must be taken to ensure that entries are as permanent and immutable as possible (there are a number of options for on-line digital notebooks that have these features). In general, notebooks should contain:

  • Enough information for a reader to determine the objective, design, procedure, and results of each experiment (even failed experiments)
  • An organizational scheme; e.g., a table of contents
  • References to where the primary data are stored

Also please note that laboratory notebooks belong to the laboratory, not the student. Discuss with your PI whether or not you are permitted to keep a copy for yourself.

See the Canvas site for more details.

Section updated on 12/03/2023.

1.7.3. Academic integrity

NGG students must abide by Penn’s Code of Academic Integrity, which aims to formalize a code of conduct that is necessary for open, honest scientific training and research. The code applies to activities are both internal (e.g., coursework, laboratory rotation talks and summary documents, TA responsibilities, and thesis work) and external (e.g., publications and conference abstracts and presentations). 

A key component of scientific integrity is source attribution. We therefore emphasize the importance of using acceptable standards of source attribution at all times. When in doubt about if or how thoroughly sources should be attributed for internally targeted documents like take-home exams, written documents, etc, be sure to ask for clarification from the course director and/or NGG Chair. In general, excessive source attribution is preferable to incomplete attribution. Moreover, unless otherwise stated, students must assume that any course assignment or test should be completed individually, without help from other students or improper outside resources.

Potential violations of academic integrity are reported to the Office of Student Conduct, which “deals with alleged instances of academic dishonesty and other student misconduct, in order to determine how best to resolve these allegations consistent with the goals and mission of the University as an educational and intellectual community.” Such violations are taken seriously and can result in suspension or expulsion from the program.

Section updated on 12/03/2023.

1.7.4 Use of Artificial Intelligence (e.g., ChatGPT)

Newly developed Artificial Intelligence (AI) tools like ChatGPT are poised to have an increasing presence in scientific education and research. These tools implement forms of generative AI, which according to ChatGPT “refers to a type of artificial intelligence that generates … outputs, such as images, text, or audio, based on a set of input data [and] a learned model” [1]. We cannot yet envision the full scope of uses and impact of generative AI on educational and research activities of the NGG. However, we anticipate that these tools could be potentially disruptive, both positively and negatively. It is thus imperative to establish guidelines governing their use by our trainees. We organize these guidelines according to two major principles, as follows:

  1. Integrity. Academic and research integrity requires respecting not just the quality but also the origins of ideas and findings. Using content generated by generative AI without providing clear and proper attribution of its origins is plagiarism. The following guidelines should be followed when using and citing these tools:
    1. Citations should always provide enough information to identify the scope of content provided by the tool and its exact origins; e.g., an in-line reference to the specific tool (including version, if possible), date, and query used (see included example).
    2. These tools generate their responses based on content published or posted elsewhere that may require credit, depending on the nature of that content and how you are using it. However, these tools currently provide little or no information about the sources of that content. Thus, identifying and citing the appropriate source(s) may take substantial additional effort.
    3. Given the breadth of possible uses of these tools, which in principle could include making an outline, a rough draft, or even a final revision of larger chunks of text, be aware that even providing full attribution, as outlined above, might not be enough to counteract claims of improper use under certain conditions. Thus, consider the implications carefully before using these tools (e.g., how will an instructor or journal react if a document you submit was based on a draft produced using generative AI?).
    4. In addition, the University, individual graduate groups, course instructors, PIs, journal editors, granting agencies, and others may provide specific policies governing the use of these tools. Be sure to check for those policies before using these tools.
  2. Usefulness. Like all tools, generative AI can potentially be useful, inconsequential, or detrimental, depending on when and how it is used. Using generative AI as a tool for any educational or research activity requires careful evaluation of its potential advantages and disadvantages and best practices. Below are some issues to consider:
    1. There is no guarantee that the outputs of generative AI are accurate or factual. Thus, any use of these tools should be combined with other approaches involving trusted sources to critically assess their outputs.
    2. At present, generative AI tools are designed to learn features of the statistical structure of their training data (e.g., whether a particular pattern of words tends to occur in proximity to another pattern of words), not any form of human- (or animal-) like reasoning about the factors, principles, or logic behind that structure. Thus, the output produced by these tools should viewed with skepticism and should not be assumed to provide meaningful or interpretable insights.
    3. Do not use generative AI as a shortcut that compromises your long-term training goals, including learning to think critically and to write clearly and in your own unique voice.

For questions or comments about these guidelines, please contact the NGG Chair or Vice Chair.

1. ChatGPT (https://chat.openai.com/), 01/15/23, in response to query: “what is generative AI, in one sentence?”

ChatGPT and Its Implications for Your Teaching from the Center for Teaching and Learning.

1.8. Leave of absence

BGS, in accordance with University policies, allows graduate students to take leaves of absence with the permission of the Graduate Group Chair and the Graduate Dean. NGG students must write to the NGG Chair requesting the leave. If approved, the request will be forwarded to the BGS Director for further approval. The main types of leave are medical, family, and paid time off for the birth or adoption of a child.

Section updated on 12/03/2023.

1.10 Letters of recommendation 

There are still some kinds of mail that are not sent electronically. The address you should use for this kind of mail is the office of the NGG Coordinator, located next to the Barchi Library: 

Neuroscience Graduate Group
University of Pennsylvania
140 John Morgan Bldg
3620 Hamilton Walk
Philadelphia, PA 19104-6074

1.10 Letters of recommendation 

A student applying for a fellowship, job, etc., should ask for letters of recommendation from faculty members with whom they have established a strong relationship and who can write knowledgeably about the student's accomplishments and plans; e.g., the PI, members of the Thesis Committee (particularly the Chair), collaborators, and/or members of the Executive Committee. Any student that has concerns or questions about finding appropriate and effective sources of letters of recommendation should consult with the NGG Chair or any member of the Executive Committee.

Section updated on 12/03/2023.


Prior to the Candidacy Exam, NGG students participate in required and elective courses, laboratory rotations, and other programmatic activities. Students will be assured of completing the required number of course units by the end of their second year if they take four credit units each semester and two credit units in the summer. Any changes to the requirements listed below, including changing or dropping courses, must be approved by the ARC.


2.1. Grades and Academic Standards
2.2. Core Courses
2.3. Elective Courses
2.4. Journal Clubs 
2.5. Independent Study
2.6. Laboratory Rotations
. . . . 2.6.1. Rotation Talk
. . . . 2.6.2. Summary Document
. . . . 2.6.3. Rotation Grade

2.1. Grades and Academic Standards

The NGG uses the standard letter grading system used by the Graduate School of Arts and Sciences to evaluate performance in courses and laboratory rotations: A (Distinguished), B (Good), C-F (Unsatisfactory/Failure), I (incomplete).

For laboratory rotations, the sponsoring faculty member submits both a letter grade and a written evaluation of the student's performance at the end of the semester, which is reviewed with the student.

A grade of Incomplete becomes 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 completed within the one-year period, then the student will be required to take an additional course to complete the requirements of the curriculum.

Grades are reviewed for all first- and second-year students at the start of the Fall and Spring semesters by the NGG ARC and by the BGS Curriculum and Standards Committee. These committees will determine an appropriate course of action for any student who receives an unsatisfactory grade (less than a B) in a course or who does not meet the University policy of a B average. In the case of a single poor grade, the student is typically placed on academic probation and required to remediate the grade by retaking the same course or an alternative course specified by the committees. Once placed on academic probation, the student must improve their academic performance or will be dropped from the program. In the case of multiple poor grades in a single semester, the committees will also consider the option of dropping the student from the program immediately.

A note on our philosophy of grades

Our overall goal is to prepare our students for science-related careers that require constant intellectual growth. To achieve this goal, our program is designed to provide new experiences and intellectual challenges at every stage of training, including courses and lab rotations in the first two years (or one year for combined-degree students) through the dissertation in the remaining years. Grades for courses and rotations are a useful metric to assess each student’s initial progress along this path, including helping to identify potential weaknesses in background or understanding that may require some extra attention or efforts to overcome. Thus, grades are a part of the minimum academic standards that our students must attain to remain in good standing in the program and ensure that they have established a core comprehension of the material encountered during the pre-thesis years to maximize the likelihood of success on their thesis research.

We therefore believe that it is important for students to take courses and rotations seriously as opportunities for growth and learning. In the process of doing so, students should use grades as a form of constructive feedback that indicates whether or not they are attaining or surpassing the minimum academic standards, and more generally can be used as a basis for establishing and refining priorities related to study habits, time in lab, etc. Students should always feel welcome to reach out to their Academic Review Committee members and members of the Executive Committee, including the Chair and the Director for Advising, with any questions about grades or how they can be used to set priorities.

Some other relevant points about grades:

1. Students should not assume that perfect grades are the obligatory outcome of hard work alone. This idea, which pertains to both courses and lab rotations, may contradict earlier academic experiences for some students and thus can come as a bit of a shock. Hard work is certainly one key factor that is used to determine grades (and success in science more generally), but it is rarely the only factor. To be a useful metric of progress, grades also must take into account other factors like depth of understanding, creativity, and productivity.

2. For our Core courses, we generally do not use collaborative or group exams. Instead, we require each student to work alone, thereby allowing us to better evaluate strengths and weaknesses on an individual-by-individual basis and ensure that each student’s training is progressing in an effective manner.

3. We do not use pass/fail in our Core courses for similar reasons: we believe that the (slightly) more extensive scale of A/B/unsatisfactory provides more precise feedback that, as described above, can be used to assess individual progress and set priorities.

4. The point has been raised occasionally that stress about getting top grades may develop from worrying about how grades might affect the ability to obtain fellowships. In our experience (including based on talking to NIH program officers about this topic), this concern is unfounded. The impact of a difference between, say, an A and B on a graduate transcript is minuscule compared to all of the other components of a fellowship application, including the quality of the research proposal and the overall training plan — which are, of course, exactly the things we are trying to optimize when we provide constructive feedback (in the form of grades) early in training.

Section updated on 12/07/2023.

2.2. Core Courses

Every NGG student is required to take four Core courses in the first year of graduate study:

  • Core I: BIOM 6000 Cell Biology (Fall) 
  • Core II: NGG 5720 The Electrical Language of Cells (Fall)
  • Core III: NGG 5730 Systems Neuroscience, including Neuroanatomy (Spring)
  • Core IV: Seminar-related Journal Club (Fall and Spring)

The purpose of these courses is to introduce all NGG students to the broad basis of modern neuroscience. Students taking Core I, II, and III must receive a grade of B– or better to obtain a passing grade. Students with strong backgrounds in any of these three Core courses may request an exemption from that course. An exemption is typically accompanied by attendance in a more advanced course in the same general area.

Core IV is required for all first-year PhD students during both the Fall and Spring semesters and for CD students in the Fall semester. This course is not taken for credit but is nonetheless a program requirement. This course helps to develop critical reading and presentation skills and is tied to the weekly MINS Seminar Series. Thus it also affords students the opportunity to familiarize themselves, in advance, with the work of the visiting speakers and to meet these visitors over lunch.

In addition, all NGG students must take the following courses:

  • NGG 6950 (Scientific Writing) in the semester of taking the Candidacy Exam (with the first workshop in the prior semester). This course helps students to prepare their Written Document for the Candidacy Exam, which is in the form of an NRSA proposal (see below).
  • NGG 6050 NeuroCore: Quantiative Data Analysis for Neuroscience. This course is offered every fall semester.

Section updated on 12/07/2023.

2.3. Elective Courses

Students are able to choose electives from all relevant, graduate-level courses offered across campus. Elective courses offered directly through the NGG, which have an “NGG ****” course listing, can be taken by any NGG student without additional permission. Courses offered by other departments or programs can be taken with permission from the ARC or NGG Chair. Some courses also require permission from the instructor. In these cases, it is up to the student to contact the instructor to obtain permission. Undergraduate courses may not be taken for graduate credit without permission from the NGG Chair and the Biomedical Graduate Studies (BGS) Office. Students are also encouraged to design their own Independent Study course to target domain-specific knowledge; see below for more details and the Canvas site for example syllabi.

Students may also take a few courses during their thesis years but must first obtain permission from their Thesis Advisor.

Section updated on 12/07/2023.

2.4. Journal Clubs

PhD students during the first year and CD students during the first fall semester are required to participate in the seminar-related Journal Club.

PhD during the second year and CD students during the first spring semester are required to participate in at least one specialty journal club in the area of their planned thesis research. Participation must include regular attendance and a presentation at least once per semester. 

Section updated on 12/07/2023.

2.5. Independent Study

Students taking an Independent Study register for course NGG 999. An Independent Study can be used as an opportunity to work with a faculty member in a structured manner with the goal of, for example, obtaining an in-depth review of relevant literature via guided readings and discussions or learning a new technical skill.

The student and faculty member are required to submit a written syllabus describing the schedule of activities to be undertaken and the form of evaluation for the proposed Independent Study. The syllabus is due within two weeks of the beginning of the semester and then must be approved by the NGG Chair and/or ARC Chair for the student to receive credit for the Independent Study. See the Canvas site for examples.

Students are encouraged to follow the planned syllabus as much as possible but also should feel free to make changes as needed throughout the semester. As long as those changes stay within the spirit of the original plans, no further reporting is needed. However, if the changes are major (e.g., switching topics or advisors; feel free to reach out to the NGG Chair or Vice Chair for guidance), a new syllabus should be provided.

Section updated on 12/07/2023.

2.6. Laboratory Rotations

Laboratory rotations provide in-depth exposure to selected areas of neuroscience and complement topics covered in classes. They also provide the means by which students select their Thesis Advisor. Rotations can lead to presentations at scientific meetings and, occasionally, to a publication. However, both faculty and students should realize that the emphasis during a laboratory rotation is on the learning experience rather than productivity. Rotation mentors typically are members of the NGG. 

PhD students are required to complete three laboratory rotations, and can complete as many as five rotations, by the end of their second year. CD students are required to complete three rotations, and can complete a fourth one, by the end of their first graduate year. 

A waiver of one laboratory rotation may be requested by students with substantial prior research experience; e.g., research that resulted in an Honor's Thesis, a publication, and/or a presentation at a national/international meeting. The NGG Chair must be petitioned in writing (limit: 1 page), including a description of the relevant prior research experience. Note that even after obtaining a waiver, the student is required to follow all of the relevant rotation requirements, such as the rotation talk and paper, as appropriate (see below), and will receive a grade and written evaluation from the mentor for each semester until the student passes the Candidacy Exam.

To set up a lab rotation, each student should contact, and if possible meet, at least six NGG faculty members. All faculty understand that a meeting to discuss a potential rotation is not a commitment to actually stay there for the rotation. If the laboratory in which you want to rotate is unavailable for the coming semester, then it is permissible to make a date for a subsequent semester. Students are encouraged to use rotations as opportunities to broaden their training and therefore should consider labs with diverse scientific questions and approaches. To help obtain such diverse training, NGG students are occasionally permitted to rotate in the laboratory of a non-NGG faculty member. However, the student must first obtain permission from the NGG and ARC Chairs.

For the Spring Semester of year 1, students have the option of completing either: 1) a single, full-semester rotation, as per previous policy; or 2) two shorter rotations, corresponding roughly to the first and second halves of the semester. Students choosing option #2 are required to have both rotations set up by the beginning of the semester. Students are encouraged to consider these options carefully, including discussing them with their ARC and potential PIs. It is likely that some students and PIs will benefit from a longer Spring rotation, whereas others will benefit from more options. 

Fall Semester rotations should be set up by the end of the 2nd week of the semester. Spring Semester rotations should be set up before the end of the Fall Semester. Summer Semester rotations should be set up by May 15.

All students are required to give Rotation Talk and write Summary Document, described below. PhD students are required to give two rotation talks: one in January (for the fall rotation) and one in September (for either spring or summer rotation, selected by the student). CD students are required to give one rotation talk in January. The Summary Documents are due one week before the corresponding Rotation Talks are held. 

Section updated on 12/07/2023.

2.6.1. Rotation Talk

Lab Rotation Talks are designed to give students the opportunity to present a prepared, short talk in a relatively informal setting and receive helpful feedback from faculty evaluators on scientific content and presentation skills. All students are required to attend the entire session of talks that includes their own talk. The talks are also open to anyone else who wants to attend.

Each talk is 10–12 min, followed by 3–5 min of questions, covering knowledge gained and work done during the rotation. The emphasis is not on the quality or quantity of data but on: 

  • Organizing background information, methods, results, and analyses into a cogent presentation.
  • Learning how to present a research talk. 
  • Answering questions, to demonstrate an understanding of the overall aims and importance of the project. 

The laboratory rotation advisor should help the student develop and rehearse the talk. The advisor is also strongly encouraged to attend the actual talk but may not participate in answering questions. 

The talks are watched and critiqued by the Rotation Talks Committee, which is composed of a Chair and several faculty members. 

The Chair:

  • Organizes Committee members for each session of talks. 
  • Assigns Committee members to give feedback on the talk and paper to particular students. 
  • Introduces each student speaker. 
  • Keeps time and stays on schedule throughout the session, giving an indication at 10, 12, and 15 minutes, and ending the question-and-answer period at the 15-minute point.
  • Ensures that verbal and written feedback is shared with the student speaker. 

The Committee members take notes on the quality of each presentation and are encouraged to ask questions of each speaker. One Committee member is assigned to provide constructive verbal and written feedback (via the Rotation Talk Evaluation Form) to each student speaker about the content and delivery of their talk as well as the content of their paper. Both types of feedback are important. Verbal feedback is provided immediately, when the presentation is fresh in everyone’s mind. Written feedback allows the students to digest the information more slowly and is also provided to the ARC, which tracks the progress of all NGG students.

Section updated on 01/15/2024.

2.6.2. Summary Document

The Summary Document is two pages long (single-spaced11-point Arial font, one-inch margins), plus a list of references (the references are not included in the two-page limit).  The Document should include the following sections (students should feel free to adjust the format within reason and possibly include a figure or two for clarity):

Name(s) of faculty advisor(s)
Your name
Semester and year of rotation

<A sentence or two describing the question or issue that motivated your work>

<A paragraph giving sufficient background for a reader to understand the context of your scientific question, including clinical and/or scientific significance>

<A sentence or two describing the primary hypothesis>

<A paragraph or so describing the approaches you used>

<A paragraph describing actual or anticipated results>

<A paragraph describing actual or anticipated results>

<Provide a complete list of References for all papers cited, using the Journal of Neuroscience format.>

Rotation Advisors are encouraged to mentor the writing of the Summary Document. The document must be emailed as an attachment to the NGG Coordinator at least one week before the Rotation Talks are held, so it can be read by the Rotation Talks Committee prior to the Talks. The Rotation Talks Committee will provide each student with brief feedback on the Summary Document, as well as on the Rotation Talk, using the Rotation Talk Evaluation Form.

Several examples are provided here.

Section updated on 12/07/2023.

2.6.3. Rotation Grade

Grades are given for the rotation at the end of the semester whether or not a project has been completed. The grade is also independent of the Rotation Talk and Summary Document, but can take into account the level of preparation for the talk and document. Grades are accompanied by a written evaluation, to be shared with the student.

Section updated on 12/07/2023.


Students choose a thesis laboratory some time during the first or second year (or first year of graduate work for CD students), typically by the Fall semester just preceding the Candidacy Exam semester. The procedure for choosing a thesis laboratory is as follows:

  • The student and mentor should have extensive discussions about possible projects, availability of funding, and general expectations of both parties (or more, if co-mentors are involved) before reaching a mutual decision for the student to join the lab.
  • Once such a decision is reached by the student and mentor(s), the student sends an e-mail to the NGG Chair indicating the student's desire to settle into that lab.
  • The NGG Chair then contacts the proposed mentor to determine the availability of funds. If sufficient funds are available, as verified by BGS, the student is officially entered into the laboratory. If funds are not available, the NGG Chair and Vice Chair will work with the student to identify an appropriate thesis lab.

Section updated on 12/04/2023.


Note: Each Student should give a copy of these Guidelines to their Candidacy Exam Committee Members when they first form their Committee.

Deadlines for 2023–2024 Academic Year

December 5, 2023, 12–2 pm: Candidacy Exam Workshop (click here for slides)
February 2, 2024: Proposal Letter due
February 16, 2024: Specific Aims returned, with feedback
February 28, 2024: Committee finalized, date set
3 weeks prior to exam: Final written document due
10 days after receiving document: returned with feedback
4 days prior to Exam: revised document submitted to Committee Chair
June 15, 2024: All Exams complete unless an extension was granted by the NGG Chair 

The transition from the coursework phase to the thesis phase of the Neuroscience Training Program is marked by the Candidacy Examination. In the Exam, the student proposes and defends a plan for the thesis research, designed to substantially advance the understanding of a basic problem in contemporary Neuroscience. 

The “Candidacy Year” is year 2 for PhD students and Graduate Year 1 for CD students. During that year, students are expected to identify their Thesis Lab by the start of the Spring semester and then complete the Candidacy Exam by July 1. Students who have not identified a Thesis Lab in time will be granted an extension by the ARC, typically for one additional semester. In general, students are expected to complete their Candidacy Exam no sooner than the second semester during which they are in their Thesis Lab. The Candidacy Exam must be completed before a student can enter Dissertation status. Failure to complete the Candidacy Exam or identify a Thesis Laboratory will result in dismissal from the program.

The Candidacy Exam consists of two parts: a written Proposal and an oral Defense. Both must reflect a substantial depth of knowledge in the topics covered by the proposed thesis research and an understanding of the broader significance of the work. Extensive preliminary data are not expected, but whatever preliminary data are available should be included. The source of all preliminary data (i.e., self or another lab member) should be explicitly indicated. Additionally, real data should be distinguished from modeled or hypothetical data. 

More specific instructions are provided in the Candidacy Exam Workshop that meets each Fall semester. This workshop consists of one or more informal group meetings of the 2nd-year PhD students, 1st- graduate-year CD students, the NGG Chair, and other NGG faculty.


4.1. Role of the Thesis Advisor and other consultants
4.2. Proposal letter
4.3. Written proposal
4.4. Candidacy proposal defense
4.5. Candidacy Exam outcome

4.1. Role of the Thesis Advisor and other consultants

The Thesis Advisor typically plays an important role in the development of the research plan by providing ideas, directions, and context. In addition, the Thesis Advisor is responsible for ensuring that the overall objectives of the Proposal are worthwhile, the proposed experiments address those objectives, and the proposal is submitted in good order and is defensible. The Advisor is permitted to give copies of current or former grant applications to the student. These documents can be used as reference material but not as templates for the student's Written Proposal. The advisor is not permitted to be involved in the actual writing or detailed editing of the proposal.

The advisor, along with members of the Exam Committee, other members of the faculty, postdocs, and students, can also be consulted for guidance and feedback on the Written Proposal and Defense. This guidance and feedback can be used to identify relevant literature, facilitate understanding of the underlying ideas, define the appropriate scope and depth of the proposed project, and point out the presence of potentially "fatal flaws" in the experimental design and interpretation. It is the student’s responsibility to synthesize this guidance and feedback and ensure that it is used to support and improve, not replace, the student’s independent contributions to the Written Proposal and Defense.

Because the issue of feedback is not always straightforward, the ARC Chair and/or NGG Chair will provide guidance on a case-by-case basis should questions arise about what is appropriate or inappropriate feedback. Moreover, the degree of the Thesis Advisor's involvement in developing the final document and the relative contributions of the advisor and student must be stated in the Candidacy Exam Proposal Report. A comparable statement is standard in all NIH NRSA applications. 

Section updated on 12/07/2023.

4.2. Proposal Letter

Each student must submit a Proposal Letter to the ARC Chair by February 1 for a Spring Semester Exam (typical), April 1 for a Summer Semester Exam, or June 1 for a Fall Semester Exam. The letter will be reviewed by one ARC member with written comments.

The letter must include the following three items: 

i) Tentative thesis title and advisor's name

ii) Specific Aims [limit: one single-spaced page]

The Specific Aims page typically begins with one or two background paragraphs that briefly summarize relevant supporting information and identify the central hypothesis or question. These paragraphs should clearly answer: What is the general context and field of study of your work? What unanswered question(s) will your research address? Why is it interesting? What do you plan to learn?

Two or three Specific Aims are then listed that describe the specific projects you plan to pursue. Each Aim should be accompanied by a brief paragraph that identifies the hypothesis, goal, and general experimental approaches and strategies.

A final sentence or two can be included that helps tie the Aims together and to your overall goals.

Note that it is perfectly acceptable for the Specific Aims to change as one proceeds through the Candidacy Examination process, as the proposal continues to be developed and discussed with the Thesis Advisor or members of the committee. It is also important to remember that, as is true with NIH grants, the Aims may evolve as the experiments are conducted.

You may include references in the Aims page. The reference list will not count towards the one-page limit.

iii) Proposed list of Candidacy Examination Committee Members

The student should include a list of 5–7 potential Committee members. This list should be generated in consultation with the student’s Thesis Advisor. However, this list should not include the Thesis Advisor, who is explicitly excluded from membership on this Committee. Because this list is merely a proposal, the student should not ask any potential Committee members in advance whether or not they wish to be included on the list. However, it can be useful to indicate why particular individuals might be appropriate (experience with a particular technique or system, etc). It is also useful to indicate one or two people on the list who could potentially serve as Chair of the Committee. The Committee Chair must be a member of the NGG. 

The ARC and NGG Chairs together will use this list to help select a Candidacy Exam Committee, which consists of a total of four members meeting the following criteria:

  • At least one Committee Member acts as the NGG representative; e.g., a former or present ARC member. These individuals have considerable previous experience with this process and thereby act to ensure expertise with and knowledge of the NGG Candidacy Exam process.
  • At most, one member with appropriate expertise may be from another Graduate Group. Their requested inclusion should be explicitly justified in a short sentence.
  • The Candidacy Exam Committee typically includes members who have broader expertise than the eventual members of the student's Thesis Committee, because the Candidacy Examination cover general topics in Neuroscience that extend beyond the focus of the proposed thesis project. 
  • To allow faculty to dedicate sufficient time and energy to each Candidacy Exam, it is desirable that no single faculty member participate in more than two Candidacy Exams during any given semester. 
  • Upon receiving the approved list of Candidacy Exam Committee Members, the student must contact them as soon as possible to schedule a date and time for the Candidacy Defense. 

Section updated on 12/07/2023.

4.3. Written proposal 

The guidelines for the written Proposal are exactly those used for the standard NIH Individual Predoctoral NRSA Fellowship application format. The limits on font size, margins, and document length must be followed. If you have any questions about these guidelines, check with the ARC or NGG Chair or the NGG Coordinator. The Proposal must include five components:

i) Cover Page [limit: one page]. This page includes the Proposal Title; the name of the student and the Thesis Advisor; a list of Candidacy Committee Members with the Committee Chair identified; a brief statement describing the roles of the student and Thesis Advisor (and others, if appropriate) in the development of the document; and the date, time, and location of the Defense.

ii) Project Summary/Abstract [limit: one paragraph]. Describes clearly, concisely, and with as little jargon as possible an overall summary of the proposed work. 

iii) Specific Aims [limit: one page]. Include two or three Specific Aims. Avoid proposing any Specific Aim that depends entirely on a particular outcome of a preceding Aim, if there is not sufficient confidence in that outcome. Instead, the Aims should complement each other, and each should be a feasible project in its own right. The Proposal should be "hypothesis driven" and thus each Aim should address a working hypothesis regarding an unresolved issue in Neuroscience. The proposal should describe work that can reasonably be done by one person in 3–5 years, not what an entire lab of people could accomplish in 3–5 years. In this respect, the written Proposal will be more focused than the Thesis Advisor's typical NIH R01 application. Remember that this document is a proposal, not a contract; thus, the Aims can reasonably be expected to change over time, with input from the Thesis Advisor and eventual Thesis Committee. 

iv) Research Strategy [limit: six pages]. The Research Strategy is divided into two sections: Significance and Approach. The Significance section describes, in a clear and concise manner, the relevant background and explains why the project is interesting and important. The Approach section should include a description of the proposed experiments, their analyses, interpretation, and possible alternative outcomes and pitfalls (including controls to test for the presence of these pitfalls, and how any pitfalls will be overcome). Preliminary data is sometimes not available and thus is not required. However, students who have collected relevant preliminary data are strongly encouraged to include it in this section, as it will increase confidence in the feasibility of the proposed experiments. 

v) Bibliography & References Cited. From the SF424 Guide: "Each reference must include the names of all authors (in the same sequence in which they appear in the publication), the article and journal title, book title, volume number, page numbers, and year of publication. Include only bibliographic citations. Applicants should be especially careful to follow scholarly practices in providing citations for source materials relied upon when preparing any section of the application."


  • The student provides each Committee Member with a final version of the Proposal at least 21 days before the Defense date. 
  • All of the Committee Members evaluate the Proposal and provide written and/or oral feedback to the student within ten days of receiving it.
  • The student then has seven days to edit the Proposal as recommended by the Committee and provide the revised version to the full Committee at least four days before the scheduled exam. The revised version should include a summary of the revisions (<1 page).
  • The Committee Chair is then responsible for evaluating the revised Proposal and reporting back to the student and the rest of the Committee at the time of the Defense about the quality and thoroughness of the revisions.

Because the Candidacy Exam is an early step in professional training, the rules will be enforced just as they would be if this Proposal were a real grant application (although not with the finality of a real grant application, which is rejected without review if the guidelines are not followed). Thus, the Committee may delay the Defense if the members receive the Proposal later than scheduled or seriously out of format.

Section updated on 12/08/2023.

4.4. Candidacy proposal defense

The Defense consists of a meeting with a Candidacy Exam Committee. This meeting is scheduled for three hours; exams are typically concluded in two to three hours.

Scheduling: Because it is always a challenge to identify a date and time at which all Committee Members will be available, scheduling of the Candidacy Defense should be done at least three months in advance. It is often most effective to use an on-line scheduling tool (e.g. Doodle, When2Meet) to identify specific dates and times that everyone—including the Thesis Advisor—can attend. Once a time has been agreed upon, the student should notify NGG staff of the meeting time and solicit help finding a room for the meeting. If the student has difficulty scheduling the meeting, then they should bring this issue to the attention of the ARC Chair. 

Preparation: Starting a few weeks in advance, the student is strongly encouraged to give practice talks. 

Role of the Committee Chair: Prior to the exam, NGG staff will share the student’s file with the chair; this file contains the student’s academic history at Penn. The Chair will bring this folder to the Defense and, if the Chair deems it useful, will discuss the student’s academic history with the other members of the Committee either at the beginning or end of the Defense when the student is not present. It is the Chair’s responsibility to ensure that during the Exam, the questions asked by the other members of the Committee and the answers provided by the student are appropriate in scope and tone. The Chair is also required to fill out the Candidacy Exam Evaluation and to meet with the student after the exam to discuss the Candidacy Proposal Outcome.

Role of the Thesis Advisor: The Thesis Advisor will attend the Candidacy Exam Defense but may not serve in an official capacity on the Exam Committee. The Thesis Advisor is not permitted to participate during the Defense unless specifically asked to do so by the Committee Chair. If the Advisor does nonetheless speak up, then it is the duty of the Committee Chair to respectfully remind the Advisor that it is inappropriate to do so unless requested. 

Agenda: The Defense begins with the student waiting outside the room while the Committee discusses their general assessment of the Written Proposal. The Thesis Advisor remains in the room for this discussion but participates only when invited by the Committee.

The Defense commences with the student beginning a formal, ~15–30 minute presentation of the proposal, including motivation, background, Aims, preliminary data (if obtained), and expected results and interpretations. At the Committee's discretion, either throughout or at the conclusion of this talk, the student will be asked questions regarding all aspects of the Proposed Research. The discussion should be expected to range widely to assess the student's ability to marshal knowledge from all areas of Neuroscience. 

At the conclusion of the exam, the student will leave the room while the Committee deliberates. The Thesis Advisor will remain present but will not participate in this discussion unless invited by the Committee. 

Section updated on 12/07/2023.

4.5. Candidacy Exam outcome

At the conclusion of the Proposal Defense, the Candidacy Exam Committee Chair completes the Candidacy Exam Evaluation Form. This report includes an evaluation of both the Written Proposal and Defense. A copy of this report is given to the NGG coordinator for the student’s academic file. 

The Committee Chair must immediately inform the student of the outcome of the exam. The Chair must also discuss in detail with the student the written comments from the Exam Report. This discussion typically also occurs immediately following the Defense but can be scheduled for a later time (but within one week of the Defense) if necessary. 

There are three possible outcomes to the Exam:

i) Unconditional pass. The student then becomes "candidate for the PhD." 

ii) Conditional pass is assigned if the Committee feels that the student would benefit by, for example, re-writing and/or re-defending part or all aspects of the proposal. In such cases, a specific duration will be assigned for the assigned modifications. In the case of a re-Defense, said event should be scheduled as soon as possible to ensure a date when all Committee Members will be available. Conditional passes should be resolved within 1–3 months following the initial exam, unless there are extenuating circumstances that have been cleared by the NGG and/or ARC Chair.

iii) Fail. Students who fail the Candidacy Exam will be told why in the most specific terms possible. Students who fail the Candidacy Exam are candidates for dismissal from the NGG. Dismissal is not determined by the Exam Committee but by the NGG Chair and the ARC. The Committee may also recommend that the student repeat the examination after a brief but reasonable period, generally near the end of the subsequent semester. If the student must re-defend the Proposal, then an additional Committee member, most likely from the ARC, may be added by the NGG Chair. 

Section updated on 12/07/2023.


The Ph.D. Thesis is the single most important component of the Neuroscience Graduate Program. It is here that the student demonstrates competence in the conduct and communication of scientific research. Thesis Advisors are drawn from within the NGG. Co-Advisors are possible but require approval by the NGG Chair. The details of the thesis problem are formulated jointly by the student and the Advisor. Completing the thesis involves forming and meeting regularly with a Thesis Committee, preparing the Written Thesis, and carrying out an oral Defense. 

Students will be granted permission to Defend only after having at least one first-author manuscript accepted for publication (i.e., already published or in press). In rare situations, the permission to defend could be granted only if 1) a first-author paper is submitted to a journal, 2) there is a reasonable plan for revision agreed to by all parties involved (including the PI, the student, and the thesis committee), and 3) the request is approved by the NGG chair.  

Students who have been granted permission to Defend should download and follow the instructions given in the NGG Graduation Checklist.


5.1. Thesis Committee
. . . . 5.1.1. Thesis Committee composition
. . . . 5.1.2. Thesis Committee external examiner
. . . . 5.1.3. Thesis Committee meetings
5.2. Written Dissertation
5.3. Thesis Defense

5.1. Thesis Committee

Each student organizes a Thesis Committee within four months of successful completion of the Candidacy Examination. This Committee must be in place at all times during the thesis years. If a student moves to a new laboratory during this time, a new Thesis Committee must be appointed immediately and must meet within three months to discuss new plans for the Dissertation research. 

Section updated on 12/04/2023.

5.1.1. Thesis Committee composition

The Thesis Committee should be composed of the Thesis Advisor (or co-Advisors) plus three additional faculty, one of which is designated the Committee Chair. The Committee should be formed as follows:

  • The student selects the Committee members, including the Committee Chair, in consultation with the Thesis Advisor. The Committee Chair should be selected before the first Committee meeting. The NGG and ARC Chairs are available if candidate suggestions are needed.
  • If the advisor is a member of the NGG, then at least two of the three additional faculty on the Committee must be members of the NGG. All committee members should have an affiliation with some BGS-sponsored graduate group.
  • If the advisor is not a member of the NGG, then all of the other Committee members must be members of the NGG.
  • The Chair of the Thesis Committee must be someone other than the advisor and must be a member of the NGG.
  • During the process of selecting Thesis Committee members and the Chair, the student should visit with each candidate, describe the proposed research, and ask if the candidate is willing and able to participate.
  • The composition of the Thesis Committee, including the identity of the Committee Chair, must be provided to the NGG Coordinator as soon as the Committee is established and before its first meeting. 

Section updated on 12/04/2023.

5.1.2. Thesis Committee external examiner

When the student is within one year of the Thesis Defense, one additional examiner must be added to the Thesis Committee. This examiner is selected by the student, in consultation with the advisor. Students are permitted to select the final examiner from within the University of Pennsylvania community. However, students are encouraged to select someone from outside of Penn (but relatively nearby, and always from within the continental U.S., to find people willing to make the trip for one or two meetings). An examiner from outside of Penn can help expand the student’s professional network, including providing letters of recommendation from another institution (grant, fellowship, and job applications can benefit greatly from not having all recommenders come from the same institution) and as a point of contact for future post-doctoral and faculty job opportunities.

The additional examiner should be added before the committee meeting at which the student intends to seek permission to defend their Thesis. The additional examiner can thus be invited to that committee meeting and brought up to speed on the state of the Thesis project. Alternatively, if the additional examiner is added after this committee meeting and/or can only attend the Thesis Defense, extra effort (e.g., Zoom, e-mail) is needed to bring that person up to speed on the state of the project well in advance of the Thesis Defense. It will be the responsibility of the Thesis Advisor to pay for this examiner to attend the Thesis Defense. 

Section updated on 12/04/2023.

5.1.3. Thesis Committee meetings

The purpose of the Thesis Advisory Committee is to provide objective advice and fresh points of view to the student and Advisor. A lively discussion may be expected at these meetings, which is sure to benefit the student and the student's research. Committee meetings are also important for ensuring that the student is: i) on schedule to complete the Thesis in an appropriate time frame, including maintaining the appropriate balance of experiments, analysis, writing, and dissemination; ii) thinking about and effectively pursuing post-graduation career plans; and iii) at the appropriate time is given permission to defend. 

Scheduling. The first Committee meeting should take place no later than one year after the Candidacy Examination. Subsequently, the Thesis Committee should meet at least once per year to review progress and make plans for the coming year. MD/PhD students are to meet at least every six 6 months. As the Thesis nears completion, it is often desirable to meet at shorter intervals. 

Because it is challenging to schedule any meeting that includes multiple individuals, please schedule all Thesis Committee Meetings at least three months in advance. 

Meeting Materials. For each meeting, the student must provide (via email):

  • A Progress Report, which is a concise written summary (no more than three text pages, plus figures) of progress and future plans, that should be given to the Committee members and to the NGG Coordinator at least one week before the meeting.
  • Lab notebooks used since the previous meeting. In keeping with BGS policy, the Thesis Committee Chair is responsible for ensuring that lab notebooks are reviewed at each meeting, either by one designated committee member or by the committee collectively. There is no expectation that lab notebooks be reviewed in their entirety. However, the committee should feel confident that the student's lab notebooks and overall data organization are complete and well managed.

    If any concern arises from the lab notebook review, then the committee will undertake a more extensive review at the earliest possible time after the committee meeting. If the committee finds that the lab notebooks are incomplete and/or poorly managed, then they should provide: i) explicit, written and verbal instructions to the student for improving the notebooks, and ii) a deadline for submission of the notebooks for re-review. It must be emphasized to the student that any modifications made to the lab notebooks should occur on separate, previously unused pages on which it is explicitly stated that supplemental notes are being made to a previous (and dated) experiment.
  • An electronic, up-to-date CV. Click here for career development resources

Meeting agenda. First, the student will leave the room so that the committee may consult with the advisor regarding progress and any concerns. Second, the student will return and the advisor will leave the room so that the committee may consult in a similar manner with the student. Third, the student then gives a prepared presentation of their progress to date plus plans for the coming year. The presentation should be designed to last approximately 30 minutes if there were no interruptions or questions (although there certainly will be).Fourth, the Thesis Committee and student will discuss the student's Individual Development Plan (IDP, discussed above).

Meeting Report. The Chair of this Committee will provide a brief written report, using the Thesis Committee Meeting Evaluation Form, summarizing the results of each meeting. This form should be filled out at the end of each committee meeting, reviewed with the student and then provided to the NGG Coordinator. 

Section updated on 12/04/2023.

5.2. Written Dissertation

The purpose of the Dissertation is to communicate effectively the results of the student's doctoral research. The Dissertation is considered a published document. However, unlike most published papers, there are no word or page limits. Therefore, the Dissertation may include speculations that are interesting but would not be permitted in a journal publication. The Dissertation must include:

General Introduction: an opening chapter that provides background, context and motivation for the research. This chapter should be approximately 10–20 double-spaced text pages in length, excluding its reference section.

Original Research: at least one chapter of original research. One of these chapters must have been accepted into a peer-reviewed journal. However, it is in the best interest of the student to have submitted as many chapters as possible for publication prior to the Thesis Defense.

General Conclusions/Future Directions: a final chapter that is different in content and in spirit from the General Introduction because it is primarily forward looking; i.e., what are the important implications of the work performed and where are they likely to lead? This chapter should be approximately 5–10 double-spaced text pages in length, excluding its reference section.

The Dissertation Document must be submitted to the Thesis Committee at least two weeks before the Thesis Defense date. The Committee members will read and assess the written document during that two-week interval and bring their edited versions of the Dissertation to the Defense.

Penn's Dissertation Manual, including formatting requirements, can be found here. A copy of Penn's Guide to Using Previously Published Work in Dissertation is here.

Section updated on 12/04/2023.

5.3. Thesis Defense

The final requirement for the PhD in Neuroscience is the Defense of the thesis before the faculty. The student should schedule the Defense well in advance, just like for normal committee meetings, and in a room large enough for the public seminar.

If a Thesis Committee member cannot attend the Defense, the student must meet with the NGG Chair to discuss the circumstances and decide on a course of action. One possible outcome is that the missing committee member must review the student's written Dissertation and submit a critique (which may include questions) to the chair of the committee before the Defense, so that those comments and questions can be included during the exam portion of the Defense and addressed in any revisions that may be made to the Dissertation.

The Defense consists of two parts. The first is a public, formal seminar. The seminar will be advertised in a manner similar to that used for MINS colloquia. Students and faculty will be encouraged to attend. The student should plan the seminar carefully and present the work in a professional manner. The talk should be limited to approximately 50 minutes in order to leave time for questions and discussion.

In the second part of the Defense, immediately after the seminar, the student will meet privately with and respond to questions posed by members of the Thesis Defense Committee. This meeting generally extends for approximately 1–2 hours. At the conclusion of the Defense, the Thesis Committee must decide to: i) Accept the Dissertation as submitted, ii) Accept the Dissertation with revisions, or iii) Reject the Dissertation. If the Committee rejects the Dissertation, then it must indicate explicitly (verbally and in writing) the reasons for the rejection and meet again after a new version has been submitted for its review.

A final copy of the dissertation must be submitted to the NGG Coordinator after you (the student) have received confirmation from your Committee Chair that no further edits are required. The final copy of the Dissertation will be bound and placed in the MINS library. Scheduling of the Defense and coordination with the Graduate School will also be handled through the office of the NGG Coordinator.

Students who have been granted permission to Defend should download and follow the instructions given in the NGG Graduation Checklist.

Section updated on 12/04/2023.


See the NGG Canvas site for forms and more information (Pennkey login required). If you require NGG Canvas access please contact the NGG coordinator.

Neuro images courtesy of NGG graduate Greg Dunn (http://www.gregadunn.com).