Initial Advising and Workshops
In the two weeks before classes start, first year students attend a series of workshops (TA orientations, safety seminar, etc.). The group of incoming students will meet with their temporary advisors and then as a group with a faculty/student advising committee to discuss their course options for the upcoming year. See Graduate Curriculum for the list of required courses. Prior to this meeting, the students should review the requirements and prepare a tentative plan. Registration for classes should be completed prior to the first day of classes. Courses may be added or dropped within the first week of the quarter.
Graduate students rotate through three laboratories during their first year (four if they do an early rotation in the summer prior to the first year). Each rotation lasts one quarter. The primary purpose of the rotations is to acquaint the students with faculty members and their labs in order to provide a basis for choosing an advisor for their Ph.D. thesis research. Students may also elect to do rotations to learn techniques or procedures that might be helpful later in their research. At the end of each rotation, the students will give a 15 minute rotation report to the Department at a forum to be scheduled during finals week. In addition, the lab supervisor will write a brief evaluation of the student's performance during his/her rotation to be placed in the student's file. At the beginning of the Winter and Spring quarters, the first year students meet individually with the Graduate Admission and Policy Committee to discuss their rotation in the previous quarter and their future plans.
It is important to note that participation in a rotation does not automatically imply that there will be funding or space within the lab for thesis research.
Choosing Laboratory Rotations
Prior to the beginning of Autumn quarter, the Department holds a two day research retreat. Besides providing a forum for the faculty and members of their groups to discuss recent research developments, the retreat provides an opportunity for first year students to hear about faculty interests before they decide on their rotations for Autumn quarter. During Autumn quarter, a series of bi-weekly meetings will be set up at which the first year students will hear research presentations by faculty members (two per meeting). These meetings are designed to provide an overview of the research projects in each lab and will provide a basis for making rotation decisions for the Winter and Spring quarters.
Choosing an Advisor
The choice of a thesis advisor is obviously an important one and is worthy of considerable care and thought both during and after the rotations. The first year students should plan to discuss thesis research opportunities with those faculty members with whom they rotate and who are doing work in their areas of interest. Students should plan to meet with appropriate faculty members on several occasions to explore the kind of research projects available and to get a sense for the way the faculty member approaches research problems and mentoring. First year students should plan to choose their thesis advisor at the end of Spring quarter. No commitments are to be made by either the students or the faculty before this time. In exceptional circumstances, a student might choose to rotate a fourth time in the summer following the first year. Students must realize that the selection of an advisor depends on numerous factors and is not a unilateral decision on either the student’s or faculty member’s part.
Most graduate students are supported from Departmental funds as RAs in their first year. In the Autumn quarter of the first year, all eligible students should apply for an NSF fellowship. In the Spring of the first and second years, eligible students are strongly encouraged to apply for a position on the MCB training grant (or any other applicable training grant). After the first year, all students are supported either as an RA on a research grant, as a trainee on a training grant, or as an NSF fellow. If a training grant or fellowship stipend provides a lower salary than the Departmental RA rate, the stipend will be supplemented to the usual RA rate from faculty research grants. In some cases, students benefit from fellowship and training grant stipends that exceed the Departmental RA rate.
Subject to availability of funds and continued satisfactory progress in the program, Ph.D. students can expect financial support for a period of up to six years. Both the advisor and the student should be aware that, following six years of residence in the Department of Microbiology, a student is not eligible for financial support from Departmental sources. Students may be supported from research grants at their advisor’s discretion after six years.
Acquiring good teaching skills is an important part of graduate training. All students are required to teach two laboratory courses in Microbiology. Generally, students teach one quarter in their first year and one quarter in their second year, but other arrangements are possible so long as the two-quarter requirement is met by the end of the second year. The Lecturer or other faculty member responsible for the laboratory course will prepare a written evaluation of the student's teaching performance to be placed in the student's file. Besides the two-quarter laboratory teaching requirement, all students are required to present at least two lectures in an undergraduate course in their third or fourth years. Arrangements for giving these lectures can be made by contacting individual faculty members. This requirement can also be fulfilled by presenting lectures in the undergraduate methods course (Micro 431, see Mark Chandler).
All graduate students are expected to sign up for and attend Journal Club on Thursdays at 11:30 (Micro 522) and the Departmental seminar on Tuesdays at 4:00 (Micro 520). Students at FHCRC may choose to attend seminars at either the UW or FHCRC to fulfill the seminar requirement. Graduate students are not scheduled to present papers at Journal Club until their third year.
Ph.D. Supervisory Committee
A well balanced committee is of tremendous benefit to the students and their advisors. At the beginning of the second year, a five person Ph.D. Supervisory Committee is appointed as follows:
1. Adviser must be Microbiology Faculty
At least two of the five committee members in addition to the GSR must be members of the graduate faculty. The make-up of the committee including a recommendation for the GSR is determined by the student and his/her advisor with final approval by the Graduate Admissions and Policy Committee. The student should forward to the Graduate Admissions and Policy Committee his/her suggestions for the composition of the Supervisory Committee by the first Monday in November of the second year.
2. Member Microbiology Faculty
3. Member Microbiology Faculty
4. Member Microbiology Faculty or Faculty member outside of the department
5. GSR outside of the department
Guidelines for Ph.D. Thesis Supervisory Committee Meetings
Research by its very nature is not always predictable and cannot be rigidly programmed. In addition, it is not always possible to anticipate potential problems at the outset. However a general series of guidelines seems appropriate to provide both students and faculty a set of standards against which student progress can be measured. Under normal circumstances, a student will complete all of the requirements for the Ph.D. degree in approximately 5 years. The following are the recommendations of the Graduate Admissions and Policy Committee for monitoring the satisfactory progress of graduate students towards completion of their Ph.D. thesis requirements. It is the responsibility of both the student and advisor to see that the annual meetings are scheduled. After each committee meeting, a member of the student's committee other than the advisor will prepare a short report that is distributed to the members of the committee and the student, and a copy is placed in the student's file.
Meetings within the second year. The first meeting of the supervisory committee with the student occurs during Spring quarter of the second year at the time of the presentation of the Topic Qualifying Exam (see below).
The second committee meeting should occur in the Summer of the second year. At this meeting the committee should review the course work with the student to ensure that Departmental requirements have been met and the Graduate School requirement of 18 graded credits has been fulfilled. The student will submit a detailed written progress report (2-3 single spaced pages) to committee members one week prior to the meeting. The report should include the Specific Aims for the proposal to be written for the general exam. This meeting is not an exam but rather should focus on the student’s progress and future plans to help the student prepare his/her research proposal during the summer. A highly focused research program will aid in the preparation of the proposal. The student should prepare a 30-45 minute oral presentation on his/her research progress and future plans. This meeting will take between 60-90 minutes.
Meeting for the oral component of the General Exam. This meeting occurs early in the Autumn quarter of the third year (prior to November 15th). See below for format.
Meeting at the end of the third year. The student will provide the committee with a 2-3 page written progress report one week prior to the meeting. In the report there should be an indication to the committee as to where the work stands in relation to his/her first publication. A requirement of the Microbiology graduate program is that the student be the first author on multiple papers related to the thesis research and which are published (or in press) in refereed journals. Under unusual circumstances, one first-author publication would satisfy this requirement. Ideally at this point the student will have a working outline for a manuscript. The student, with the help of the supervisory committee, will discuss the immediate direction of the research in the context of the overall research plan, as described in the original proposal for the oral exam. Any redirection of the research or serious problems should be discussed. Any deficiencies or problems identified at the time of the oral exam will be reviewed with the student at this meeting.
Meeting at the end of the fourth year. The student should provide the committee with a 2-3 page written progress report and copies of any publications (or in press papers) one week prior to the meeting. By this time, the student is expected to have at least one first author paper published or in press and another manuscript in progress. The meeting will therefore center around discussions relating to the completion of the thesis research, particularly in the context of how the work will be published. The student should provide an outline of the experiments needed to be carried out during the final year. If the student plans to finish up within 3-6 months of this meeting, he/she should provide an outline of the proposed thesis and seek approval from the committee to begin writing the thesis at that time.
Meeting at the end of the fifth year (or just prior to writing the thesis). At this meeting the progress report should include a detailed outline for the thesis. The time line for completion of the thesis and for the thesis defense should be presented. Approval of the committee is required prior to the writing of the thesis. Ideally 2-3 first author papers should be published or submitted for publication. Any problems with progress towards completion of the thesis research should be addressed at this time. If progress is marginal, the committee should spell out what must be accomplished over a defined time frame for the student to avoid final probation and/or dismissal with a Master’s degree.
Meeting at the end of the sixth year. If the student is still not finished at this point, the supervisory committee will consider two alternatives at this meeting.
The student should provide a firm date for the defense and provide a final thesis outline. Unless there are extenuating circumstances, laboratory research should be completed by the end of the summer quarter following the meeting.
In the event the research progress has not been satisfactory, the supervisory committee must consider placing the student on final probation or immediately dismissing the student with a Master’s degree.
General Guidelines for a Non-thesis Master’s Degree
Although the Department does not admit students specifically into a Master's degree program, occasionally a student will leave the Ph.D. program with a Non-thesis Master's degree. The specific requirements for the Master's degree are determined by a three-person Master's committee composed of the student's research advisor and two additional members of the Microbiology faculty. The student should have fulfilled the course requirements for the Ph.D. degree and will generally have done the usual rotations required of a first year student. Typically the student will carry out research for a minimum of 3 additional quarters and present a 2-3 page written report (or manuscript for publication) to the committee one week prior to an oral presentation of his/her work.
Format for the Topic Qualifying Exam
Purpose. The objectives of the Topic Qualifying Exam are for the student (i) to gain an understanding of a topic area unrelated to his or her thesis research, (ii) to present a written critical review of previous work and devise a logical plan for future research directions in this alternative topic area, and (iii) to effectively present the topic and respond to questions in an oral setting.
Procedures. Students should submit a short paragraph describing two choices for topics to the Graduate Admissions and Policy Committee by the first Monday in November of their second year. The following procedure is intended to assure that the topic is suitably different from the thesis area: First, the student should designate the topic area that best fits their thesis. Then, the student should propose alternative topics that do not fall into the thesis topic area. Topic areas are defined as follows: bacterial pathogenesis; biochemistry; computational biology; astrobiology and environmental microbiology; eukaryotic cell biology; fungal pathogenesis; parasitology; genomics and proteomics; immunology; microbial physiology and genetics; and virology. The student should also include a statement briefly describing the probable thesis topic and pointing out how the proposed alternate topics differ from the thesis topic. The committee can approve both topics (in which case the student can choose), select one of the two, or request two new topics for review.
The student’s Ph.D. Supervisory Committee plus one additional Microbiology faculty member that has been approved by the Admissions and Policy Committee will administer the exam. The additional member will be determined based on the alternative topic area and will provide scientific diversity to the examining committee. After the Ph.D. Supervisory Committees are appointed (December of second year), the student is encouraged to submit two names to the Graduate Committee for consideration as the additional member of the examining committee.
The topic examination will consist of two parts to be completed by April 15th of the second year. The first part will be a written critical review of the topic with three sections: an introduction and background section (2-3 pages), a section describing the current state of the field reflecting key research findings (2-3 pages), and a future directions/research plan section identifying critical unanswered questions and approaches to addressing them (1-2 pages). The research plan should be hypothesis-driven, organized into 2-3 specific aims, and include some mention of potential pitfalls and alternative approaches. The paper should be submitted to the committee two weeks prior to the scheduled oral presentation. Within one week, the committee members will read the paper and individually provide feedback to the student. This student will then have one week to respond to any criticisms and improve the paper (if necessary) before the oral presentation.
The second part of the Topic examination will be oral. The presentation must be given at a time scheduled to allow at least four members of the student’s committee, plus the additional member, to attend. The GSR may be invited but need not attend. A member of the committee other than the student's advisor will be chosen as the chairperson of the meeting. The presentation should be from 30 to 45 minutes, with allowances for interruptions, followed by questions. The entire exam should not exceed 90 minutes.
Evaluation. The student will be evaluated on the organization of the presentation, critical analysis of the papers discussed in depth, clarity of the discussion of experiments and future directions, and the effectiveness of the presentation style. Feedback to the student will be provided immediately after the exam by the examining committee. If the performance is considered to be unsatisfactory, the committee may require the student to repeat all or some aspects of the topic and presentation prior to proceeding to the research proposal and oral exam. The chairperson will provide a written evaluation that will be distributed to the student and other members of the committee and placed in the student's file.
Research Proposal. The research proposal, which will be focused on the students’ thesis work, should follow the format specified for an NIH grant application. This proposal should be prepared during the early part of the Autumn quarter of the third year. A set of guidelines for writing the proposal entitled ”Suggestions for Preparation of Research Proposals for General Exam" will be provided. The student should present a draft of the proposal to his/her advisor at least three weeks prior to the oral exam. The advisor will critique the draft proposal with the student and indicate any sections that need rewriting. The advisor will not, however, participate in a substantive way in the writing process. One week prior to the oral exam, the final version of the proposal will be given to each member of the student's Supervisory Committee.
Format for oral exam
Prior to the oral exam and in the absence of the student, the advisor will review the student’s academic record and give the Supervisory Committee members a written evaluation of the student's research performance and potential (see attached form). The advisor will also discuss the evaluation with the student prior to the exam. The evaluation should include an assessment of the student's effort level, creativity, independence, lab techniques, ability to design and execute experiments, and ability to communicate.
The oral exam is chaired by a member of the Supervisory committee other than the advisor or the GSR. The advisor will not examine the student but will be present and available for comment or clarification when needed.
The research proposal will provide the starting point for the oral exam, but the questioning can extend into related topics, including experimental techniques. The oral exam begins with a 30 minute presentation by the student summarizing his or her research progress and indicating future directions of the research. Although the length of the presentation is limited to a maximum of 30 minutes, an allowance will be made for interruptions by committee members who have brief questions. Following this presentation, members of the supervisory committee will examine the student in areas both related to his/her research and when appropriate, areas outside. The meeting may last up to three hours total.
At the end of the oral exam, both the student and student's advisor will leave the room. This allows the committee to discuss the performance of the student in the absence of the advisor. The outcome of the general exam will be determined solely by the committee members in the absence of the advisor. At the end of the deliberations both the student and the advisor will be called back into the room.
The decision made at the end of the oral exam is a cumulative one, taking into account the student's performance in all areas since entering graduate school. These include, in the order of relative importance: (1) the performance on the oral exam in the area of the student's research, (2) the quality of the research proposal, (3) the advisor's written evaluation of research progress and potential, (4) the performance on the Topic Qualifying Exam, and (5) the performance in course work.
The final decision must be one of the following: Pass, Fail, or Re-examine. If the committee feels deficiencies exist that need to be corrected, the “Re-examine” option must be chosen rather than awarding a “Pass” with stipulations concerning the deficiencies. A "Fail" means the student must leave the Ph.D. program, generally with a non-thesis M.S. degree. Regardless of the outcome of the exam, the members of the Supervisory Committee as well as the advisor are responsible for providing feedback to the student after the oral exam. A summary of the Committee’s decision will be placed in the student’s file.