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Training Information For Chemical and Physical Biology Program

This page presents policies relates to students.

Policies related to faculty can be found here.

 

Information for Students Entering the Program

The first year of graduate school (G-1) occurs in either the Quantitative and Chemical Biology Program

(QCB), the Interdisciplinary Graduate Program (IGP), or the Medical Scientist Training Program (MSTP).

In the spring of the G-1 year, students apply to the CPB Program by submitting: a one-paragraph description of their intended area of research; a statement of interest in the CPB program; and a list of their intended coursework in G-2. The academic transcript from the G-1 year, interest statement, research description, and coursework proposal are reviewed by the Graduate Education Committee (GEC). The GEC will review the research description to ensure its congruity with the goals of the CPB program. If the research description is appropriate and the student has performed suitably in G-1 courses, the GEC will recommend that the student be admitted to the program. They will also review the proposed courses, paying particular attention to the area of intended research and the track requirements; they may recommend alternative or additional courses during the G-2 year. If the applicant has a GPA of less than 3.0 or a grade lower than B in any required course, the student may be considered for admission, but only under probationary status. In this case, the student and mentor will be required to propose a remediation plan.

General Requirements of the Graduate School

  • At least 24 didactic hours
  • At least 72 total hours

Program Requirements of All Students

Students typically enter the CPB through either the Quantitative and Chemical Biology Program or the Interdisciplinary Graduate Program.  Some of the courses listed below will have been completed during that phase and are indicated with an asterisk.  Counseling regarding appropriate elective coursework should have began during that phase of the student’s education.

  • Responsible Conduct of Research
  • CPBP 8306: Introduction to Chemical and Physical Biology or for IGP students, the basic biomedical science curriculum, or for MSTP students, the basic medical sciences curriculum
  • Two semesters of a seminar courses
  • The requirements of a programmatic track

All students must maintain the following minimum requirements:

  • All students must maintain the following minimum requirements:

    • GPA of at least 3.0

    • Grades of B or higher in all required courses

    • No grade of F in any course

    • Professional conduct in his/her interactions with peers, faculty, and the program

    • Grades of Satisfactory for all research units

    If one or more of these requirements have not been met, the student will be placed on academic probation.  The student and mentor must ensure that the DGS is made aware of the deficiency. The student and the mentor will collaboratively propose a remediation plan to the DGS and the GEC. The plan should include, at minimum: coursework that will be taken to meet the student’s didactic requirements; a description of how the student’s approach will change; what steps the mentor will take to support and monitor the student’s progress; the timeline for correcting the deficiencies;

    A plan for reporting on the student’s progress to the DGS. The plan must be approved by the DGS. The student will remain on academic probation until the plan is successfully executed. If the plan is not achieved within the proposed timeline, the DGS will recommend the student’s dismissal from the program to the GEC and the Program Director. If the DGS, GEC, and Program Director decide that the student should be dismissed, the student will be notified as soon as possible and the reasons for the decision will be indicated. The student is allowed to petition this decision to the Senior Associate Dean for Biomedical Research Education and Training and/or the Graduate School. If the student accepts the decision, the student and mentor may petition to pursue a MS degree.

Track-Specific Didactic Requirements

Please see the table here.

RESEARCH EXPECTATIONS

Students are expected to demonstrate satisfactory progress toward the completion of the dissertation in each semester, as determined by their mentor and thesis committee, and display professional conduct in their interactions with peers, faculty, and the program. Progress is rated as satisfactory or unsatisfactory. The student must have completed a sufficient body of work to merit a Ph.D. degree, reflected in a minimum of one first authored publication in a peer reviewed journal. The committee determines that the student is ready to write up the final version of the dissertation and defend.

The program holds a retreat (typically in May of each year) that is organized by the Graduate Student Association. The purposes of the retreat are to foster communication between CPBP students and faculty and provide students with experience in presenting their work in a scientifically critical, but personally-supportive setting. The CPBP requires that all students and faculty attend the retreat. Absences require permission of the DGS and Program Director.

TRAINING FOR THE PROFESSION

All students are affiliated with the corresponding graduate training programs associated with their track, which provides each student with an essential, seminar-based forum for disciplinary and professional training in their respective field. Each of the four training programs is sponsored by a Center or Institute: the Chemical-Biology Interface training program (Vanderbilt Institute for Chemical Biology); the Molecular Biophysics training program (Center for Structural Biology); the VUIIS Research Seminar of the Imaging Institute training program (Vanderbilt University Institute for Imaging Science); and the Quantitative System Biology seminar series (Quantitative Systems Biology Center).

PROGRESS TOWARDS THE DEGREE

  • After joining the CPBP. Each student accepted into the CPBP is expected to begin their research immediately after matching to the mentor’s lab. The student and mentor should begin formally discussing the aims of the project and the potential composition of the qualifying exam (QE) committee by the January of the first year after joining the thesis laboratory. The DGS must approve the research topic and the committee in advance. To obtain these approvals, the student sends by March 15 an abstract of the proposed dissertation research and a list of possible committee members to the DGS and Program Manager before contacting the proposed committee members.
  • Pre-qualification and qualification exams. The student should begin scheduling the pre-qualification and qualification exams immediately after receiving approvals from the DGS. A pre-qualification meeting must be held with the QE committee before June 1 of the G-2 year, and the QE must be held before October 1 in the G-3 year (or equivalent). The student will provide their Specific Aims page to each member of their qualification exam (QE) committee one week prior to a one-hour pre-qualification exam meeting. The Ph.D. advisor must attend the pre-qualification exam meeting and advise the committee regarding the nature of the proposed aims, in particular the degree of independence in developing the aims. At this meeting the student will present their QE proposal aims to the committee in a presentation that includes no more than one introductory slide and one slide per aim. The committee will determine whether the student’s anticipated QE research proposal (based on the Specifics Aims) will be “defendable” in a QE. If not, the committee will help the student to craft aims that appear to be defendable. This adjustment of aims can take place either at that meeting or immediately following via iterative e-mail. The committee will also preview with the student the likely types of questions that will be asked at the actual oral QE. The student should schedule the QE timeslot to be 2 hours, with 90 minutes for the examination and the remaining time for the committee deliberations. The QE is composed of a written document and an oral defense. Students must have successfully completed at least 24 didactic units, including a grade of B or higher in all program- and track-required courses, before becoming eligible to take the QE. The QE proposal also serves as the basis for the thesis proposal. Following the successful completion of the QE, the aims of the proposal can be amended as the research evolves with the approval of the thesis committee.
  • Formation of the Thesis Committee. The student, in consultation with the thesis advisor and the DGS, selects a dissertation committee, often the same as the QE committee plus the research advisor. The committee must be chaired by a member other than the research advisor. A minimum of 4 faculty members is required (not counting the advisor), at least three of whom will be from CPBP and at least one of whom must be from outside of CPBP. Committee members who cannot be present in person for a meeting should make every attempt to participate via video conferencing. If not possible, then the committee member should communicate their evaluation to the chair after reviewing the student’s progress report and any other relevant documentation.
  • Ongoing Thesis Committee Meetings. A meeting of the thesis committee needs to be held within 9 months of the QE and then at intervals of no more than 12 months going forward. The student is responsible for scheduling thesis committee meetings and failure to have a meeting within the time frame specified at the previous committee meeting is grounds for assigning an unsatisfactory evaluation. The student is required to submit a written progress report to the committee at least two weeks in advance. The student can and should have feedback from the mentor about this report before it is sent out. The committee meeting itself consists of a formal oral presentation, typically following the written document, wherein the student defends their progress, results, and conclusions to the committee. The student can and should get feedback from the mentor regarding the oral presentation prior to the meeting. Following each committee meeting, the committee chair will draft a letter summarizing the outcome of the meeting. The chair may ask the student to prepare the first draft of the letter. The letter is circulated to all committee members for approval. In addition, the committee will complete a SACS student evaluation form. The final summary letter and SACS form should be uploaded into REDCap system.
  • Procedures to address unsatisfactory progress. If at any point a thesis advisor feels that the student’s progress or conduct have been unsatisfactory, the mentor should notify the student, the student’s thesis committee chair, and the DGS in writing. The student, mentor, and committee chair will then meet. If the student’s progress and/or conduct remain unsatisfactory at the end of the semester, the mentor should assign a grade of Unsatisfactory. The reasons for this grade must be specified in a written letter to the student. The letter should also include specific recommendations regarding how the student can improve performance. The letter should be signed by the thesis advisor and committee chair. A copy of the letter should be sent to the CPBP Director, the DGS and the Program Manager. The DGS will notify the GEC, who may make additional recommendations to the student and/or thesis advisor. Once the letter is received, unless extenuating circumstances exist, the DGS will place the student on academic probation, and they will remain on probation until the student’s research progress or conduct is deemed satisfactory. In addition, the committee chair will set up a meeting of the thesis committee to be held within 45 days. If the committee determines that progress or conduct is unsatisfactory, the DGS will meet with the student, mentor, and chair individually and then recommend how to resolve the situation. The DGS may also take these steps earlier in the process at the request of the student, mentor, or chair or at their own initiative. After the first committee meeting, a follow-up committee meeting must be scheduled within 6 or less months. If at the second meeting, the committee determines that progress or conduct of the student remains unsatisfactory, the student will be dismissed from the program.
  • Master’s Candidates. Students may elect to change their status from PhD to MS student and obtain a Master of Science (MS) degree in CPBP. This may occur when a student changes career goals or fails to complete one or more of the program requirements successfully. The latter case may include two failing grades in the QE, two grades of Unsatisfactory during the candidacy phase, or failing the final defense. To switch to the MS degree, the student and mentor need to file a single written petition with the program that includes: the reasons for the change in status; the student’s CV and academic transcript; research abstract; if a MS dissertation will be written, a list of two or more proposed readers, one of whom may be the mentor. The petition will be reviewed by the DGS and GEC and they make a recommendation to the Program Director, who is responsible for the final decision. In all cases, the student must have completed the required 24 didactic units, with a minimum GPA of 3.0 and no grade below C, and at least 6 research units. If the student has successfully passed the QE, they may obtain a “Masters in passing”. If not, then the student may obtain a MS degree by writing up their work in the form of a thesis. The thesis must be approved by the research mentor and at least one other member of the graduate faculty and it must be in a format acceptable to the Graduate School. A presentation of a public research seminar is made describing the scientific work leading to the thesis.
  • Thesis Defense. Candidates for the Ph.D. are required to write an ‘acceptable’ dissertation as defined by the Graduate School. The dissertation must add to or modify in a significant way what was previously known in the area of research. The student must have completed a sufficient body of work to merit a Ph.D. degree, reflected in a minimum of one first authored publication in a peer reviewed journal. The committee determines that the student is ready to write up the final version of the dissertation and defend. The advisor will provide input on the format and content and review the entire document. The dissertation must be distributed to the committee at least two weeks in advance. The thesis committee will be responsible for administering the final public defense and for the final evaluation of the dissertation. The chair of the committee will provide written notification to the DGS of the results of the defense. Provided that all other requirements have been satisfied, the DGS will notify the Dean of the Graduate School that the student has completed the requirements for the PhD degree.

Eligibility To Schedule Qualifying Exam

Students must have successfully completed at least 24 didactic units, including a grade of B or higher in all program- and track-required courses, before becoming eligible to take the QE.

Purposes of Pre-Qualifying and Qualifying Exam

The purpose of the CPBP QE is to evaluate the student and the proposal. The student is evaluated by examining the following with performance expected at a level typical for a G-2 student:

  1. Scientific knowledge in areas relevant to the proposal
  2. Ability to think critically and creatively about this knowledge, identifying critical gaps in the state of knowledge within a field
  1. Define important scientific objectives to fill those gaps
  2. Ability to formulate a research plan based on those objectives
  3. Research progress since joining their laboratory
  4. Other evidence of ability to complete a body of work appropriate for a Ph.D. in a typical time frame.

In evaluating the proposal, the committee will seek answers to following questions:

  1. Is the subject matter of the proposal appropriate for a PhD degree in CPB?
  2. If the aims of the proposal are successfully accomplished, would the results constitute a significant contribution to knowledge in this area?
  3. Does the proposal demonstrate innovative thought and/or methods?
  4. Is the design of the studies suitable to address the aims?
  5. Does the research proposal clearly communicate anticipated outcomes, potential pitfalls and alternative strategies.

Written Proposal Format

The general format for the written proposal is that of an NIH R-grant application with a Specific Aims page plus a 9-page Research Strategy that includes Significance, Innovation, and Approach. When preliminary data are included, the student should make clear who was primarily responsible for collecting the data. References do not count in the 9 + 1 page limit. A 30-line abstract is also required.

The format should be 11 point arial font with 0.5” margins. The student is expected to consult with his or her advisor when developing the aims. However, the student is expected to have written the rest of the proposal without input from the mentor. The student is advised to examine the review guidelines for NIH R-grant applications found at: https://grants.nih.gov/grants/peer/critiques/rpg.htm.

The written document must be distributed to the Committee, DGS, and Program Manager 2 weeks prior to the exam.

The student will provide their Specific Aims page to each member of their QE committee one week prior to a one-hour pre-qualifying exam meeting. The Ph.D. advisor must attend this meeting and advise the committee regarding the nature of the proposed aims, in particular the degree of independence in developing the Aims. At this meeting the student will present their qualifying exam proposal aims to the committee in a presentation that includes no more than one introductory slide and one slide per Aim. The committee will determine whether the student’s anticipated qualifying exam research proposal (based on the Specifics Aims) will be “defendable” in a qualifying exam. If not, the committee will help the student to craft Aims that appear to be defendable. This adjustment of Aims can take place either at that meeting or immediately following via iterative e-mail. The committee will also preview with the student the likely types of questions that will be asked at the actual oral qualifying exam.

Prior to the Qualifying Exam

The Southeastern Association of Colleges and Schools (SACS) requires each program to demonstrate ongoing efforts to assess student performance and to use these assessments to effect programmatic improvements as warranted. There are special forms used for the QE and thesis defense. The process is now online using the Research Electronic Data Capture (REDCap) system. Full instructions are found on the CPB website; briefly, the student emails themselves  an invitation to complete the REDCap survey for the QE and forwards to the committee chair.

Qualifying Exam Format

The QE is attended by the student, committee, and DGS; the student mentor is not permitted to attend the oral exam. The DGS and committee meet privately in order to review instructions for the exam and written proposal. The student is then invited back into the room and the oral exam begins. The total duration is up to 90 minutes. Of this, the first five minutes may be used by the student for a brief presentation. The student may present three slides to facilitate the presentation. Animation of the slide is allowed, but not to circumvent the 3-slide limit. The slides should be of the student’s own design and content. Typically, the slides include the Specific Aims, any key preliminary results, and key aspects of the experimental design or methods. The content and style of the oral exam can vary, but typically includes questioning on the background material related to the proposed project, explanations of the technical details of methods, questioning about expected results and contingency plans, etc. Areas of deficiency that were noted from the written document may be followed up upon. After the conclusion of the questioning, the student is asked to leave the room while the committee deliberates on the outcome.

Potential Outcomes

The exam’s outcome is based on the committee’s opinions of the proposal and the student’s performance in the oral exam. There are 3 possible outcomes:

Pass is awarded when all aspects of the student’s performance on the exam are deemed acceptable and appropriate for a 2nd year graduate student at Vanderbilt. There may be deficiencies, but they are deemed by the committee to be minor in nature.

Conditional Pass is awarded when most aspects of the student’s performance on the exam are deemed

acceptable and appropriate for a 2nd year graduate student at Vanderbilt, but there is one area of major deficiency. The committee and the DGS determine the conditions and time frame that must be met for the grade to be converted to a Pass. If the conditions are not met, the grade is instead converted to Fail. The conversion to Pass or Fail must be made within 30 days of the date of the QE.

Fail is awarded when there is more than one area of major deficiency. In the case of failure, the

student is given up to six months to retake the examination. The examining committee, in

consultation with the DGS, determines the date for the reexamination. Within a month of the first exam, the DGS will meet with the student and mentor to review the outcome and recommendations. Reexamination requires a second written proposal and oral exam. Failure to pass a second qualifying examination results in dismissal from the PhD program. In this event, the student may petition for an MS degree.

After the committee completes its deliberations and assigns an outcome, they complete a SACS QE evaluation survey via the REDCap System. The student is then invited into the room and the committee communicates the outcome of the exam and discusses the SACS form with the student. When the SACS survey is completed, the REDCap system automatically generates an email invitation to upload a letter describing the outcome of the exam. The letter should be completed within one week of the exam date. The letter is authored by the committee chair and agreed to by all members of the committee. Regardless of the outcome, the letter should indicate those aspects of the exam in which the student performed well and those aspects of the exam in which deficiencies were noted. This should include strengths and weaknesses of both the student’s performance and the proposal itself. In the case of deficiencies, their severity should be indicated and a mechanism for the student to improve his/her performance should be proscribed.

The letter will also include the next steps to be taken.

Pass: The committee makes a recommendation for scheduling the next committee meeting within 3-9 months.

Conditional Pass: The conditions to be met and their timeline for completion are indicated.

Fail: A statement is provided of the policies for re-taking the exam and potential consequences if a grade of Pass is not earned. A second attempt needs to be made within 6 months of the original QE. The letter and the student evaluation form will become part of the student’s permanent record.

SACS evaluation forms

The Southeastern Association of Colleges and Schools (SACS) requires each program to demonstrate ongoing efforts to assess student performance and to use these assessments to effect programmatic improvements as warranted. There are special forms used for the QE and thesis defense. The process is now online using the Research Electronic Data Capture (REDCap) system. Full instructions are found on the CPB website; briefly, the student emails themselves an invitation to complete the REDCap survey for the QE and forwards to the committee chair.

Guidelines and Expectations Regarding Ongoing Committee Meetings

A meeting of the thesis committee needs to be held within 9 months of the QE and then at intervals of no more than 12 months going forward. The student is responsible for scheduling thesis committee meetings and failure to have a meeting within the time frame specified at the previous committee meeting is grounds for assigning an unsatisfactory evaluation. The student is required to submit a written progress report to the committee at least two weeks in advance. The student can and should have feedback from his/her mentor about this report before it is sent out. The report should include: 1)

the abstract; 2) updated Specific Aims; 3) 1-2 paragraph summary of the student’s overall progress; 4) detailed summary of the student’s progress since the last committee meeting; 5) areas of concern that were identified in the last meeting and how they have been addressed; 6) other tangible evidence of progress, such as manuscripts, presentations, workshops, or conferences attended. The committee meeting itself consists of a formal oral presentation, typically following the written document, wherein the student defends their progress, results, and conclusions to the committee. The faculty advisor

should only intercede to clarify uncertainties or bring up salient additional points. The student can and should get feedback from his/her mentor regarding the oral presentation prior to the meeting. Following each committee meeting, the committee chair will draft a letter summarizing the outcome of the meeting. The chair may ask the student to prepare the first draft of the letter. The letter is circulated to all committee members for approval. In addition, the committee will complete a

SACS student evaluation form. The final summary letter and SACS form should be uploaded into REDCap system.

Personal Initiative and Responsibility

Students are expected to act in a proactive and professional manner throughout their tenure in the program. The faculty and staff administrators of the program are there to assist and support the students, but the student is the one primarily responsible for his or her own education. Students are responsible for:

1. Meeting all track requirements and ensuring these requirements are completed prior to the,Qualification Exam (QE). Students supported by training grants must ensure that they also meet the specific requirements of the training program.

2. Scheduling their QE and being fully aware of all policies and procedures.

3. Scheduling committee meetings within the timeframe indicated in the report from the previous meeting.

Over the course of the program, students are expected to: (i) become expert in the knowledge and skills

needed to complete their project as well as areas related to their projects; (ii) develop the ability to

solve problems independently; (iii) generate and adhere to time schedules; (iv) be responsive to

feedback from their advisors and committees.

Responsible Conduct of Research (RCR)

Students must practice RCR in all of its forms. These areas include: declaring and managing conflicts of interest; behaving ethically with regard to human and animal experimentation, authorship and publication, collaborative research, peer review, and data acquisition, analysis, and management; maintaining appropriate mentor/mentee relationships. Upon, matriculation into the CPB, must provide evidence of having received basic RCR training. Ongoing RCR training and discussions are imperative throughout CPB training.

Attendance, Holidays, and Vacation

Students are expected to adopt the work habits of successful professionals in their field. This includes working beyond the 40-hour, Monday-Friday work week as needed. Students must be willing to commit enough time for making progress in the laboratory, reading the scientific literature, assisting with other laboratory projects, etc. CPB students are entitled to time off in a manner consistent with Vanderbilt’s policies. Students are strongly advised to work closely with their thesis advisor to plan time off for vacation, personal days, etc. Communication with the thesis advisor and members of the laboratory is also imperative for absences due to illness, particularly if these require an extended period away from the laboratory.

Publication

Disseminating knowledge in oral and written form is an important component of the research and training process. When the student and advisor deem a research project to be complete, the work should be submitted for peer review and publication. Students and advisors share authorship on publications that result from the student’s activities within the advisor’s research group. Students are expected to contribute to a timely publication of the work. It is strongly recommended that students work to prepare drafts of manuscripts well in advance of completing all research.

Service

Service is an integral part of all scientists lives. Graduate student service may: serve as a mentor to undergraduate students or junior graduate students; provide service to their research group, the public or their scientific communities; serve as a member or officer of the CPB Graduate Students Association; assist in recruiting new students to their programs; serve on committees at the program or university levels; or engage in other similar activities.

Individualized Development Plans

In keeping with NIH policy, as well as the CPB’s commitment to the training and education of our students, all graduate students and their mentors are required to develop and complete a yearly Individualized Development Plan (IDP). The IDP is one mechanism through which graduate students and their mentors communicate about the student’s progress, career goals, and plans for the upcoming year. IDP forms are available on the BRET Website. Students and their mentors submit the form to the Director of Graduate Studies (DGS) and Program Manager by the end of May. The DGS will review each student’s form and communicate any thoughts back to the student and mentor by the end of June. The form itself contains specific instructions, which students and mentors should read carefully before starting the process. Contact the DGS with any questions.

ADVISING AND MENTORING

  • In keeping with NIH policy, as well as the CPBP’s commitment to the training and education of our students, all graduate students and their mentors are required to develop and complete a yearly Individualized Development Plan (IDP). The IDP is one mechanism through which graduate students and their mentors communicate about the student’s progress, career goals, and plans for the upcoming year. IDP forms are available on the BRET Website. Students and their mentors submit the form to the Director of Graduate Studies ( DGS) and Program Manager by the end of May. The DGS will review each student’s form and communicate any thoughts back to the student and mentor by the end of June. The form itself contains specific instructions, which students and mentors should read carefully before starting the process.
  • Faculty are expected to be excellent advisors and mentors to their students, providing them with education and training in the relevant research techniques and approaches, research skills of successful scientists and professional behavior. Faculty should have ongoing discussions about the responsible conduct of research with their students, discussing both general principles and the specific application of these principles to their research area. Faculty are expected to commit adequate time to mentoring students and to place a high priority on the student’s professional development. When a research project is deemed complete, advisors are expected to contribute to a timely publication of the work. Advisors should set and communicate their expectations for students in advance, maintain appropriate mentor/mentee relationships, keep a professional demeanor during all interactions with the student, and practice other behaviors that lead to positive professional relationships and student growth and development. When conflict occurs, faculty are expected to participate actively and productively in the procedures for resolving these conflicts.
  • It is recognized that there may exist scientific or other issues that interfere with the student’s progressor with the mentor-student relationship. The student may feel that their progress is being impeded in some way or is being unfairly evaluated, or that their intellectual contributions are not being fairly acknowledged. Before students have a thesis committee, the student should consult with the DGS and/or Program Director. Students who have already qualified should discuss scientific concerns with the chair of his/her dissertation advising committee. Other concerns may be brought directly to the DGS or the Program Director. Students are strongly encouraged to communicate any concerns while are in problems are still in their early stages.
  • On certain occasions, changes in mentorship may be deemed necessary. The process for changing advisors can be found here: https://medschool.vanderbilt.edu/bret/changing-research-groups/ .
  • Details on auxiliary mentoring can be found here: https://medschool.vanderbilt.edu/bret/auxiliary-mentoring/ .