Please read the latest message from the Chair with regards to the Department’s response to the Covid19 Pandemic.

All graduate oral exams will go ahead online using Zoom. It is our hope that in most cases we can stick with the original times and dates however we can reschedule them by a week or two for those students who feel that they need more time. Please contact Carrie Harber if you have any questions.


The University and the department accept that a candidate for a Ph.D. degree “shall present a thesis embodying the results of original investigation conducted by the candidate …. The thesis shall constitute a significant contribution to the knowledge of the field.” (from the SGS Degree Regulations page).

Time Frame
Permission to Write
Format of Thesis
Editorial Input from the Supervisor
Thesis Approval Form
Exam Request Form
Scheduling Exam
Membership of the Examining Committee
Distribution of the Thesis
The Senate Oral Defense
The Vote
Post-Exam Requirements
Departmental Funding Policy for students defending
Tuition Fees for Final Year Doctoral Students

Poster presentation during Research Day

Time Frame

When nearing completion of experimental work, the student must schedule a committee meeting to obtain approval to write his/her Ph.D. thesis. Permission to write, via final Committee Meeting Report Form or signed and dated Permission to Write Form, signifies that the student, supervisor and committee members agree that the experimental work required for the thesis has been completed (see section on committee meetings).

A student will have six months between receiving permission to write the thesis and the date of the Ph.D. Oral Examination. This includes three months to write the thesis, one month to revise and obtain approval from the supervisor and committee members via Thesis Approval and Exam Request Forms, and two months for the exam to be scheduled.

It is expected that the student will consult with his/her supervisor and, where appropriate, with committee members throughout the planning and writing of the thesis. The student should include in his/her discussions with his/her supervisor the time frame expected for completion of various stages of the thesis as well as the total time required.

It is reasonable for the student to expect to receive comments from his/her supervisor and committee members within two to three weeks after providing them with the thesis. If agreeable with the supervisor and committee members, it may be more expeditious to seek approval on a chapter-by-chapter basis rather than waiting until the entire thesis is written.

Time frames will vary depending on the number of revisions required, the availability of committee members, and the student’s writing skills. However, if the Ph.D. Oral Examination and any required corrections/modifications to the thesis (including final submission to the SGS) have not been completed within six months of receiving permission to write, the graduate stipend may be withdrawn.

If the student feels that he/she will require additional time to complete the thesis (i.e. he/she is approaching the six month deadline between permission to write and submission of the Thesis Approval and Exam Request Forms), the student should discuss this with his/her supervisor well before the deadline and apply to the Chair and/or Graduate Coordinator for an extension. The supervisor may agree to continue funding if there is clear evidence of continued progress towards completion of the thesis.

In the event of unusual delays (e.g. health problems, family crisis etc.), the student should consult with the Graduate Coordinator.

The student must allow for a total of NINE WEEKS from the time he/she provides the Graduate Program Administrator with all the required information until the earliest exam date.

The Graduate Program Administrator requires three weeks of this time to schedule the exam and send the exam request to SGS. SGS requires a minimum of six weeks from being first notified of the exam request until the examination date.

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Permission to Write

The student must obtain permission to write once his/her supervisory committee has agreed that the student has completed all necessary experiments needed for writing the thesis.

Permission to write must be explicitly written on the final Committee Meeting Report Form (see section on committee meetings above). This indicates that the supervisor, committee members and student all agree that the experimental work required for the thesis has been completed.

All students who have approval to begin writing their thesis must complete and submit a Permission to Write Form (this form can be obtain from the graduate office).

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Format of Thesis

The department has no rule as to the number of research chapters that constitute a Ph.D. thesis. As a general guideline, however, a thesis includes three research chapters. Generally, at least two of these typically represent published or publishable material. Often one of the chapters presents unpublished material. There are many exceptions to this guideline.

The thesis can be organized in either of the following ways:

i) Traditional Style

Introduction (in which the pertinent literature is reviewed and the problem or hypothesis stated), Materials and Methods, Results, Discussion, Conclusions or Summary, Bibliography and Appendices.

ii) Publishable Style

Discrete chapters, each in a format suitable for submission for publication. Papers already published may be used without major modifications but reprints may not be bound into the body of the thesis.

General Introduction and Discussion sections should be included, as well as Conclusions or Summary. The Bibliographies of the individual chapters may be combined, as may be the Methods sections, if appropriate.

One significant difference from a manuscript prepared for publication is that figures must be included at the appropriate places in the text. The student must obtain SGS guidelines from the Graduate Program Administrator on appropriate formatting of the thesis, or by visiting the SGS website.

The thesis should also include a title page, Abstract, Table of Contents, List of Figures, List of Tables, and List of Abbreviations. Students may find it useful to consult previous theses from their labs or to check past theses collected in the departmental seminar room.

The student must not hard-bind the thesis prior to completion of the Senate Oral Examination (coil-binding is acceptable).

A Doctoral thesis is generally organized into the following sections:


Although the length of the introduction is somewhat field-specific, in most cases 40-60 double-spaced pages of text should be sufficient. The last section of the General Introduction in either format should provide a clear rationale for the thesis project.

Title Pages and Data Attribution

If any one other than the student has contributed data to the thesis the student should clearly state this on the title page of the relevant Results Chapter(s). The student should indicate the nature of the contribution (e.g. technical assistance under the student’s guidance; independent design and interpretation of specific experiments in the Chapter etc.). If the work has been published or submitted, the full citation should also be given on this page.

The student must obtain any required copyright permissions, which may be needed for work that has been published. Journals often require specifically-worded citations to be included on the first page of the relevant Results Chapter. The student will need to submit the copyright permissions to SGS when submitting the final thesis.


Sufficient details of the methods should be given such that the research could be readily reproduced.


The quality of halftone figures must allow for unambiguous assessment of the data.


Most examiners prefer that the bibliography include titles.


Appendices may be included to cover such topics as additional details pertaining to Methods; speculative ideas; projects-in-progress; and/or negative results, particularly if the second format is chosen.

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Editorial Input from the Supervisor

Throughout the preparation of the written document, the student should be in regular consultation with his/her supervisor. It is not unusual for a student to submit individual chapters to his/her supervisor once they have been completed. Indeed, the editorial input of the supervisor during the writing of the Ph.D. thesis is considered to be an essential part of the student’s training.

Therefore, except under exceptional circumstances and provided that the SGS time limit has not been exceeded, all students will be expected to maintain their full-time (on campus) status in their respective laboratories until their thesis is complete. Completeness means that the thesis has been approved by the supervisory committee and has been submitted to the members of the senate oral committee.

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Thesis Approval Form

When the thesis is nearing completion, the student should consult with his/her supervisor and the Graduate Program Administrator about necessary documents and protocols for setting up the Senate Oral Defense (e.g. arrangements for the External Examiner, date of the final oral examination etc.).

After writing the thesis, the student must obtain written approval of the thesis from his/her supervisor via the Thesis Approval Form obtained from the Graduate Program Administrator (included in the Ph.D. Defense Package); at this point the student can give his/her thesis to the supervisory committee members to read.

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Exam Request Form

Once the supervisory committee members have read and approved the thesis via the Thesis Approval Form, the student can begin completing the Exam Request Form.

The student should carefully read the information regarding exam dates and the External Examiner. The student and his/her supervisor should decide on an appropriate External Examiner and the supervisor should contact this person to confirm that he/she is willing and able to write the appraisal and to come to Toronto for the defense.

The student should discuss possible dates for the defense with his/her supervisor, committee members and the External Examiner.

Once the Exam Request Form has been completed and signed by the student and supervisor, it must be brought to the Graduate Program Administrator who will seek approval by the Graduate Coordinator. At this time, an electronic copy of the External Examiner’s CV should be forwarded to Carrie Harber, the Graduate Program Administrator (

Note that it is the supervisor’s responsibility to host the External Examiner.

The student will have a maximum of six months from the permission to write date to prepare his/her thesis and schedule the defense (i.e. submit the Thesis Approval and Exam Request Forms). Scheduling of the exam will take approximately two months.

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Scheduling the Exam

The examination will not be scheduled until:

  1. the student has completed all course and seminar requirements;
  2. the thesis has been approved to go forward to an oral defense;
  3. the Graduate Program Administrator has received the permission to write (via final committee meeting report or Permission to Write Form), Thesis Approval Form and an Exam Request Form signed by both the student and supervisor;
  4. and the Graduate Program Administrator has received an electronic version of the thesis abstract and an up-to-date CV from the External Examiner.

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Membership of the Examining Committee

Although the student and his/her supervisor give suggestions for the composition of the examination committee on the Exam Request Form, the composition is not final until approved by the Graduate Coordinator. SGS rules state that the maximum number of voting members is six and that a quorum is four voting members.

The examining committee will normally have the following composition:

  • the External Examiner (VOTING member);
  • the supervisor (NON-VOTING member);
  • the co-supervisor, if relevant (NON-VOTING member);
  • two members of the supervisory committee (VOTING members);
  • if the student has more than two faculty on the supervisory committee the additional members can attend as NON VOTING members of the examination committee;
  • one other Biochemistry faculty member (VOTING member) **Transfer / Qualifying exam chairs excluded**;
  • one non-Biochemistry faculty member from a cognate department who has not been involved with the supervision of the thesis or collaborated with the work therein (extra-departmental, VOTING member);
  • a Chair of the exam who is assigned by SGS (NON-VOTING member).

A formal appraisal of the thesis is written by the External Examiner who must be from outside of the University of Toronto and who, except under exceptional circumstances, must agree to attend the final Ph.D. Senate Oral Defense.

SGS rules require that the External Examiner’s appraisal be available two weeks before the examination is to take place. The appraisal will be distributed to the student and to the members of the examination committee but not beyond this group. The student is not permitted to discuss the appraisal with members of the examination committee until the examination takes place.

If the appraisal has not been received two weeks prior to the exam date, the department will ask the student if he/she is willing to proceed despite the delay in the receipt of the appraisal. If the student agrees, he/she will be asked to sign a waiver. If the student does not wish to proceed, the oral exam will be postponed.

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Distribution of the Thesis

It is the student’s responsibility to ensure that the External Examiner receives a copy of your thesis at least six weeks prior to your exam date. The student should give a copy of the thesis to all other members of the examining committee at least four weeks prior to the exam date.

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The Senate Oral Defense

Before the start of the oral exam the student will give a 45 minute seminar summarizing the results of his/her Ph.D. thesis research. In addition to the members of the examination committee, this seminar is open to the public. All graduate students and members of the faculty are encouraged to attend.

At the end of the seminar the student may take questions from the audience but not from members of the examination committee.

Once the open seminar has been completed, the Senate Oral Exam will proceed in camera with only the examining committee and the Chairperson.

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The Vote

Students should consult the Guidelines for the Doctoral Oral Final Examination or the SGS Calendar for information on the voting procedure at a Ph.D. defense . In brief, the student passes if there is no more than one negative vote or abstention.

If minor corrections in style are a condition of acceptance of the thesis, the supervisor will inform the student of the necessary corrections and the student must complete these corrections within one month of the date of the examination. The supervisor must notify the School of Graduate Studies directly in writing that the required corrections have been made. A copy of this letter must go to the Graduate Program Administrator who will then forward it to the Graduate Coordinator, before the student will be recommended for the Ph.D. degree.

If minor modifications are a condition of acceptance of the thesis, the Chair of the examination committee will appoint a subcommittee of the examination committee to supervise the proposed modifications. The student will be given a statement detailing the modifications required, which must be completed within three months of the date of the oral examination. If all members of the subcommittee approve the completed modifications, the student will then have passed his/her Senate Oral Defense.

The convener of the subcommittee must certify in writing to the School of Graduate Studies within three months of the original examination, with a copy of the letter going to the Graduate Program Administrator, that the modifications have been satisfactorily completed.

Students should consult the SGS Calendar for the rules that apply if the modifications are not acceptable. If there is more than one negative vote or abstention, or if major changes are required, the examination must be adjourned. In the event of adjournment, the examination committee must provide the student, as soon as possible, with a written statement that indicates the reasons for adjournment and the committee’s requirements for a reconvened oral examination.

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Post-Exam Requirements

Immediately after the exam, the SGS Chair of the examination will take the post-exam paperwork to the SGS Ph.D. office.

Before the student submits the final copy of the thesis, he/she must obtain any required copyright permissions. This may require inclusion of a line of text at the beginning of the Results Chapters, if they’ve been published.

The student must also ensure the thesis is formatted according to SGS guidelines.

The student must submit the corrected, formatted thesis in an electronic format to the School of Graduate Studies through T-space, the University’s digital library repository, along with payment of the required thesis processing fee.

The student must submit a Library Authorization Form to the Doctoral Office at the School of Graduate Studies. Students should also consult the Electronic Theses and Dissertations Checklist on the SGS website.

Students should visit the SGS website for detailed information on all topics discussed above pertaining to producing a thesis.

The department requests that the student also produce a bound copy of his/her thesis for addition to the departmental library of theses housed in the departmental seminar room.

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Departmental Funding Policy for students defending

Students who receive Permission to Write shall continue to receive funding provided that they defend within the specified timelines as follows:

PhD Students: A student will have a maximum of 6 months between receiving permission to write the thesis and the date of the Ph.D. Oral Examination. This includes three months to write the thesis, one month to revise and obtain approval from the supervisor and committee members via “Thesis Approval” and “Exam Request Forms” and two months for the exam to be scheduled.

Funding breakdown (living allowance + tuition)

Living allowance:  The living allowance will continue to be paid up to and including the month the defence is held.

Tuition:  tuition is based on the date the final thesis is submitted to the School of Graduate Studies. Note that the thesis submission can only be done AFTER the defence and as such students should allow sufficient time for these corrections to be made and approved (1-2 weeks minimum for minor corrections).

PhD students: Final year fee’s are pro-rated on a monthly basis and are determined by the submission date of the thesis. The deadline is the 15th of the month.

No tuition: Submission of the final thesis by September 15th

After September 15th, the total tuition will be calculated monthly So for example, a student who submits their thesis between Sept. 16 – Oct. 15th will be charged 1 month, Oct. 16 – Nov. 15 charged 2 months etc.  The actual monthly total will be posted on the Student Account website.

NOTE: the fee’s for students (MSc and PhD) on a program extension will be different as they will reflect the reduced tuition of extension students. These will also be listed on the Student Account website.

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Tuition Fees for Final Year Doctoral Students

Academic fees for Doctoral students in the final year of their program are pro-rated and based on the 12-month academic year.

Doctoral students will be billed for the annual fee but may choose to pay:

  1. the full fee,
  2. the minimum first payment or
  3. the expected monthly fee.

Incidental fees are charged on a sessional (term) basis. Doctoral candidates who complete all degree requirements (i.e. defend and submit a final thesis with all corrections and modifications approved), by mid-September/mid-January do not pay fees for the fall/winter session.

After mid-September, a monthly fee will be charged for each month in which all degree requirements are not completed.

For detailed information refer to the Student Accounts website.

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