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====== PhD in Computational Sciences (PhD.CSCI) Graduate Student Handbook ======

**{{ :grads:phd_graduate_committees_.pdf |PhD.CSCI Graduate Committees}}**

**[[https://calendar.uoguelph.ca/graduate-calendar/graduate-programs/computational-sciences/|PhD.CSCI Graduate Calendar]]**

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===== Duration of the Program =====

A typical PhD.CSCI student is expected to complete the program in 12 semesters (4 years). At least 5 semesters of full-time study must be completed in the doctoral program.

Please refer to the Graduate Calendar for details regarding [[https://calendar.uoguelph.ca/graduate-calendar/general-regulations/registration// | Program Duration Schedule.]]

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===== Graduate Teaching Assistant (GTA) Assignments =====

Many graduate students are guaranteed up to 2 GTA assignments per year in their initial offer of admission (Fall and Winter semesters). While some graduate students may not be guaranteed GTA job assignments, all full-time, registered graduate students are eligible to apply for these positions.

Whether you are guaranteed GTAs or not, if you want a GTA position you must apply online each semester via [[https://www.uoguelph.ca/sessional_ta/ | GTA Work Assignments website]].

**Policy on Working with Another Supervisor**

As soon as there is interest in planning to work with another advisor (internal or external to SoCS), please discuss with your advisor the time that will be required by you and the external advisor to work on such an endevour first. A timeframe should be created so that the advisor can ensure it will not impede the student’s thesis research. The advisor must be given an opportunity to participate in and benefit from the work at no financial cost. In particular, they will be invited to participate in any resultant publication.

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===== Course Requirement =====

==== Learning Module Requirements ====
 
Based on the recommendation of the Advisory Committee, students may be required to take one or more non-graded Computational Study Modules (online tutorials) to upgrade their knowledge of different aspects of computing. Online learning modules are intended to supplement the student’s knowledge of computing and provide an introduction to aspects of computing which the student will need in order to complete their degree. The current learning modules are: 
 
  * Introductory Programming 
  * Operating System Tools 
  * Data Management 
 
The modules are intended to be a self-study experience. A description of learning objectives is associated with each module, as an interface between the student and examiners. The Co-advisors are responsible for determining if the candidate is required to take any of online learning modules, in which case the module(s) must be assigned within the first two weeks of the student’s first semester. 
 
The student is encouraged to complete assigned modules before the end of the first semester, as The student will be tested on the modules during their Qualifying Exam (QE).

* {{ :grads:phd_datamanagement_learningmodule.pdf |}}
  * {{ :grads:phd_python_learning_module.pdf |}}
  * {{ :grads:phd_linux_os_tools_learning_module.pdf |}}

==== Additional Course Requirements ====
 
Besides the learning modules, if it is determined that the student does not have sufficient preparation for their degree, they will be required to take one or more undergraduate or graduate courses. As the QE is expected to occur in semester three, the Advisory Committee is encouraged to assign courses that are as early as possible.

In addition, completion of the Technical and Communication Research Methodology Course [[https://calendar.uoguelph.ca/graduate-calendar/graduate-programs/computational-sciences/#coursestext|CIS*6890]] is required during the first year PhD students are enrolled in the program. This course seeks to help students understand the links between different disciplines, and to appreciate the diverse interpretations and techniques involved in identifying and solving interdisciplinary research problems.

**Please refer to the [[https://calendar.uoguelph.ca/graduate-calendar/graduate-programs/computational-sciences/ | PhD Graduate Calendar]] for further details.**

**One Health Collaborative Specialization**

A PhD.CSCI student enrolled in the [[https://calendar.uoguelph.ca/graduate-calendar/collaborative-specializations/one-health/#coursestext| One Health Collaborative Specialization]] is required to take the following three grad courses below [1.5 credits]:

* CIS*6890 Technical Communication and Research Methodology [0.50]
  * ONEH*6000 One Health Approaches to Research [0.5]
  * ONEH*6200 Doctoral Seminar in One Health [0.5]

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===== Advisory Committees =====
 
Each PhD.CSCI candidate conducts thesis research by working closely with __two__ thesis advisors, a School of Computer Science (SoCS) Advisor and an Application Discipline (AD) Advisor, who share equal responsibility in advising the student. At least one of the Co-Advisors must be Regular Graduate Faculty at the University of Guelph.

//The two advisors must be appointed when the student is admitted. The Advisory Committee must be established no later than the mid-point of the Student's second registered semester.//

Your advisory committee should meet with you at least once each semester. Be proactive about asking for committee meetings. Once the Advisory Committee has been approved, no changes may be made to its membership without the approval of the student's current Advisory Committee and Graduate Coordinator.

**For detailed information on Advisory Committees, please refer to {{ :grads:phd_graduate_committees_.pdf |PhD Graduate Committees}}**

[[https://uoguel.ph/ogpsadvisorycommittee| Advisory Committee Appointment & Graduate Degree Program Form (Gryphform)]]

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===== Seminar Requirement =====
 
PhD.CSCI students must give two publicly announced research seminars on their PhD thesis research. Each seminar will be scheduled by the Graduate Program Assistant (GPA) and will take place no less than two weeks after the seminar request is submitted. For each seminar, a request must be completed by the student and submitted to the GPA that includes the following:
  * Title of the Abstract
  * Body of the Abstract
  * Names of the selected Seminar Committee members     
  * A tentative preferred time & date (after confirming with Seminar Committee members)

//The Seminar Committee is composed of the SoCS advisor, who will act as Chair, the Application Discipline (AD) advisor, and one other Graduate Faculty member. It is recommended that the entire Advisory Committee attend.//

Each seminar room will be booked by GPA for 90 minutes. The presentation should be 30 to 40 minutes long and followed by questions from the Seminar Committee. The seminar is graded on a pass/fail basis. Each member of the Seminar Committee gets one vote. An abstention is regarded as a fail vote. The student is deemed to have passed the seminar if there is at most one fail vote. They must attempt the seminar again if they receive two or more fail votes.

==== First Seminar ====
 
The first seminar is intended to be an exploratory look at the student’s research area. It may include a literature review and a survey of the research area. This seminar should be presented in Semester 2, and must be successfully completed before the Qualifying Exam (QE).

==== Second Seminar ====

The second seminar is intended for students to present their preliminary research results to get feedback on both their presentation and their progress towards the thesis defence. This seminar must be presented after the QE, prior to the thesis defence, and should normally be presented before the end of Semester 7.

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===== PhD Qualifying Examination (QE) =====

The PhD Qualifying Examination (QE) is intended to assess the PhD candidate's knowledge and preparation to perform the research necessary for their studies. All candidates will be required to participate in an Oral Component related to their research Proposal. Candidates who were required to take one or more Learning Modules will have a Written Component based upon the material from the Modules.

//The QE should be completed by the end of the student's fifth semester.//

The QE can only be held after the student has successfully completed the first seminar and any required coursework specified by the Advisory Committee. Arrangements for the QE should be made **at least 4 weeks prior to the anticipated date of the QE oral presentation.**

**Please refer to the [[https://calendar.uoguelph.ca/graduate-calendar/degree-regulations/doctor-philosophy/| Qualifying Examination Regulations]] in the PhD Graduate Calendar for more details.**

==== Qualifying Exam (QE) – Written Component ====

In the case where a student has been required by the Advisory Committee to take one or more Learning Modules, the QE will include a Written Component. It consists of questions related specifically to the Learning Modules, and serves to ensure that the student has the necessary computational skills to successfully perform the proposed research.

For each required module, there will be one written test which will be a maximum of 2 hours.  The QE Committee is responsible for setting the test(s) two weeks prior to the Oral Component.   All tests must be completed one week before the Oral Component. The outcome of the Written Component can be one of the following: the student passes the component or the student fails the component.  If the student fails, they may be required to retake one or more modules and the corresponding tests.

==== Qualifying Exam (QE) – Oral Component ====

A {{ :grads:qe_request.pdf | Qualifying Exam Request form}} AND written QE Research Proposal must be submitted **at least 4 weeks prior to the date of the anticipated oral presentation.** The QE Request Form should include a recommendation from the Advisory Committee that the student's potential as a researcher and research performance to date are satisfactory. The QE Committee must receive the final Research Proposal for review at least two weeks prior to the QE.

* The QE Research Proposal must contain the following items:

- A survey of appropriate background literature. 
  - A description of the proposed research. 
  - A statement describing the merits and scholarly value of the proposed research. 
  - A schedule of the research program that the candidate will follow which includes a sequence of milestones and objectives. 
  - It is encouraged that thought be given to risks associated with the Proposal, and considerations of backup plans and fallback positions be included to protect against worst-case scenarios.  
  - The Proposal should have a maximum of 50 pages, excluding references and appendices. It should be formatted with 12 point font, 1.5 spacing, and 1 inch margins on all sides.

* Questions during the Oral Component will be based upon the Research Proposal. They are designed to test the candidate's general knowledge of their broader research area and to test their specific knowledge related to the Proposal.

* The Oral Component consists of a 30 minutes oral presentation by the candidate followed by questions (maximum 90 minutes) from the Exam Committee (total 120 minutes long).

* The oral presentation is announced publicly and is open to public attendees (followed by a short question period from the audience). The question and answer period is open to the public (for observation), with questions from ONLY the Examination Committee (2 rounds of questions with a short break in between, if needed). The deliberation period is closed.

* For detailed information on Qualifying Examination Committees, please refer to {{ :grads:phd_graduate_committees_.pdf |PhD Graduate Committees}}
  * {{ :grads:qe_request.pdf | Qualifying Exam Request form}}
  * Please review {{ :grads:qe_guidelines_for_oral_presentation.pdf | Qualifying Examination Guidelines for Oral Component}} for timing details for the QE

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===== Preparing your PhD Thesis =====

When preparing your PhD thesis, please ensure you follow one of the following guidelines for format, style and organization:
  * For students who prefer using Word, please use the [[https://www.uoguelph.ca/graduatestudies/current-students/preparation-your-thesis | Graduate Studies Guidelines]]
  * For students who prefer using LaTeX, please download the {{ :grads:guelphthesisphd.zip |PhD Thesis Template for LaTeX}}

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===== PhD Thesis Defence =====

Arrangements for the PhD thesis defence should be made __**[[https://graduatestudies.uoguelph.ca/current/completion/thesis_completion/doctoral_sched | at least eight weeks prior to the anticipated date of the defence.]]** __

Below you will find the steps and forms that are required for a PhD Thesis Defence. The defence is expected to be no more than 3.5 hours in length, consisting of a 30 minute oral presentation by the student followed by questions from the Examination Committee.

* **Please refer to the OGPS website for more information on [[https://graduatestudies.uoguelph.ca/current-students/preparation-your-thesis|preparation of your thesis.]]**

*  **Please see {{ :grads:guidelines_for_oral_examination_of_thesis_-_msc_phd.pdf |Guidelines for Oral Examination of Thesis}} for the timing details of the defence**

==== A. Advisory Committee Approval & Request for Examination (Defence) ====

The student must first provide the Advisory Committee with a copy of their PhD thesis for review and approval.  Once the Advisory Committee has approved the thesis, all members of the Advisory Committee must sign the Examination Request Form. Once completed, the Examination Request Form must be submitted to the Graduate Program Assistant **at least 8 weeks prior to the anticipated date of the defence. **            
 
**To initiate the PhD Examination (Defence) Scheduling Process, the GPA will require the following:**
 
  *   [[https://www.uoguelph.ca/graduatestudies/sites/uoguelph.ca.graduatestudies/files/exam_request%20a.pdf | Examination Request Form]]

*   {{ :facultystaff:forms:grad_faculty_nomination_form_-_f23.pdf | Graduate Faculty Nomination [Exam Committee]}}

* {{ :facultystaff:forms:external_examiner_nomination_updated_2023_.pdf |PhD External Examiner Nomination}}

*   Tentative date range for the defence

*   Mode of delivery: Students have the option of conducting defences online or in-person

==== B. TurnItIn ====
     
All graduate students have access to [[http://turnitin.com/| TurnItIn]], whereby students can upload their thesis drafts for instant plagiarism analysis. Students must register using their @uoguelph.ca email address (all others will be deleted). The 'course' you should register in is called **"Graduate Research 2024-2025"**.  The class id and enrollment password are:

* Class ID: 41253109
  * Enrollment password: SoCSRules

==== D.  Examination Committee ====

Preparations to begin forming the Examination Committee for the PhD Defence will begin once the [[https://www.uoguelph.ca/graduatestudies/sites/uoguelph.ca.graduatestudies/files/exam_request%20a.pdf | Examination Request]] (including a tentative defence date range), Graduate Faculty Nominations and External Examiner Nominations have been submitted to the GPA.

The GPA will work with the Graduate Progress Committee to establish and approved the Examination Committee.  Once the Examination Committee is formed, the examination will be officially scheduled.

The candidate must have the final version of their thesis submitted directly to the GPA via email (this will be the version of the thesis shared with the Examination Committee). **The Examination Committee requires at least 4 weeks to review the thesis prior to the scheduled oral defence**.

== External Examiner Nomination ==

The student's Advisor is responsible for submitting the External Examiner nominations to the Graduate Program Assistant. The External Examiner Nomination should include the names of //at least three// nominated external Graduate Faculty, each of which have been contacted by the Advisor and have confirmed availability for the tentative defence date(s). The Graduate Progress Committee will review and approve the External Examiner selection from the nominations provided by the Advisor.

Responsibilities of the External Examiner include:
  * Reviewing the student's thesis and preparing a report prior to the PhD defence.  The External Examiner must send the report to the SoCS Director at least 7 days prior to the defence.  This report will also be sent to the student and Advisory Committee (not the other members of the Examination Committee) for review. The student is not required to revise the thesis prior to the defence.
  * Participating as an active examiner on the student's PhD Defence Examination Committee

**For detailed information on Examination Committees, please refer to {{ :grads:phd_graduate_committees_.pdf |PhD Graduate Committees}}**

**{{ :grads:phd_thesis_-_external_examiner_nomination.pdf |External Examiner Nomination}}**

SoCS follows the [[https://calendar.uoguelph.ca/graduate-calendar/degree-regulations/doctor-philosophy/ |Office of Graduate and Postdoctoral Studies thesis guidelines]] for PhD Defences.

==== E. Notification of Defence ====

Notice of the defence will be sent by the GPA (at least one week prior) to the SoCS Faculty & Graduate Students email listserv and advertised on the News & Announcement section of the [[https://www.uoguelph.ca/computing | SoCS website.]]

==== F.  Thesis Completion ====

Upon successfully passing a PhD Defence Oral Examination, students must follow the [[https://www.uoguelph.ca/graduatestudies/current/completion/thesis_completion | thesis completion instructions]] on the Graduate Studies Website. This includes uploading the thesis to the [[https://atrium.lib.uoguelph.ca/ | Atrium]].

**[[https://www.uoguelph.ca/graduatestudies/current/completion/submission_checklist | Graduate Studies Thesis Completion Checklist]]**

The School of Computer Science (SoCS) does not require a bound copy of the student's thesis.  Students can still get a bound copy for themselves through [[http://www.pageforpage.com | PageforPage]], M & T Printing Group (email your request to ryans@mtprint.com) or at Staples.

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===== Applying to Graduate =====
 
Make sure you review the [[https://www.uoguelph.ca/registrar/calendars/graduate/current/sched/index.shtml | Graduate Calendar]] for important dates, such as:

*     Last date for application to graduate for Convocation without late fee 
  *     Last day for program completion for Convocation; includes thesis submission, final grades 
  *     Last day to submit late application for Convocation

**As soon as you are ready to defend, please ensure you [[https://www.uoguelph.ca/graduatestudies/current/completion/graduation|apply to graduate]] online.**

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==== Early Refunds ====

Depending on when students defend/submit their final thesis, registration for the following semester and fee payment may be required.  Please refer to  [[https://www.uoguelph.ca/registrar/studentfinance/fees/refunds_guelph_gr | Student Financial Services]] for dates and deadlines.

If students successfully defend their thesis before the end of the current semester, they may be entitled to an [[https://www.uoguelph.ca/graduatestudies/sites/uoguelph.ca.graduatestudies/files/early_completion_rebate%20a.pdf | Early Completion Rebate]]. Please also refer to the official [[https://www.uoguelph.ca/registrar/studentfinance/fees/refunds_guelph_gr | Student Financial Services Rebate Schedule]].

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