1.          Induction Program

Students registered as full time OIST PhD students complete an induction program during their first week of enrollment (known as Enrollment Week). This program includes briefings on the PhD program, available student support, IT infrastructure, and use of the library and laboratories (including occupational health and safety).  Mandatory online training and a preliminary health screening must also be completed before access is provided to research laboratories.

All OIST PhD students enrolling in any given term must attend Enrollment Week in full, at the time scheduled by the Graduate School. Any PhD student unable to do so must defer to the following term, if allowed by the Dean of Graduate School.

Incoming non-regular students will be provided an induction program at other times of the year as appropriate. 

No laboratory access will be provided to students who have not completed this induction program.

 

2.          Gap Program for Full-time PhD Students

The OIST Graduate School may offer a Gap Program to full-time incoming PhD students (who have formally accepted OIST offer of enrollment) prior to enrollment in the PhD program.  Eligible students are those who require a greater proficiency in English in a laboratory setting, or those who require preliminary experience in a laboratory environment.

Students are not automatically eligible for enrollment into the Gap Program.  An offer to join the Gap Program will only be made to an incoming student after consideration of each individual student’s circumstances.  If there is no added educational benefit to a student, the student will not be eligible to enroll in the Gap Program.

The Gap program is available for a maximum period of one term.  The Graduate School will to the best of its ability assign students to an English-speaking laboratory as close as possible to the student’s proposed field of research, toward the improvement of English communication skills in science and technology.  Students will also be able to attend English courses at the OIST Language Education Section when available.

Please note that space availability in units may limit the number of Gap program places that can be offered.  Interested students are encouraged to apply as soon as possible to maximize the possibility of a placement being found.

Rules concerning financial support for the Gap Program are separately stipulated.

 

3.          Mentor Assignment

An OIST faculty member, as close to the student’s proposed field of study as possible, is assigned to each student as a Mentor prior to arrival on campus.  The Mentor is required to work carefully with the student to select courses and lab rotations that reinforce the foundations of the proposed field of study, and to provide the necessary scientific background to develop the ability to collaborate across traditional scientific boundaries.  Each Mentor is appointed by the Dean of the Graduate School with advice from the Academic Affairs Section.

During the first two years of enrollment the Mentor will be available to meet regularly with the student to discuss any difficulties the student may have with coursework and lab rotations, or to discuss any general welfare concerns.  It is recommended students meet with their Mentor at least once per term. 

After progression to thesis research, the Mentor will continue to play a mentoring role for the duration of the student’s enrollment as a member of the student’s Thesis Committee.  The Mentor cannot also be the student’s Thesis Supervisor.  If a student elects to undertake their thesis research in the research unit of the Mentor, a new Mentor shall be appointed.

3.1         Development of Academic Plan

In discussion with the Mentor, students develop their own course curriculum, including lab rotations, based on their educational background, intentions, and experience.  The Academic Plan is developed to be completed within two years.

The Academic Plan will consider any transferable credits, specific experience and research interests of the student, and Mentors will ensure students meet OIST curriculum requirements.  The Academic Plan will be submitted to the Academic Affairs Section by the student.

3.2         Mentor Report

A meeting between student and Mentor is required at least once per year (for the first two years of enrollment), and a Mentor Report is to be submitted to the Academic Affairs Section by the mid-point of each academic year of years 1 and 2 of enrollment (calculated from the student’s starting term).  Note that the Mentor is responsible for alerting the Graduate School of any difficulties the student may be facing, and that cannot be solved locally.

 

4.          OIST Curriculum Requirements

Students with a Bachelor’s degree are required to attain at least 30 credits, including all mandatory credit-bearing elements of the program, in order to graduate.  Students with a STEM-related Master’s degree are required to attain at least 20 credits, including all mandatory credit-bearing elements of the program, in order to graduate.

The OIST curriculum includes mandatory and elective courses (the latter including both basic and advanced).  20 credits for Bachelor’s entry (10 for Master’s entry) must be attained through elective coursework.  10 credits are attained through mandatory requirements of the curriculum; including Professional and Career Development courses, submission and examination of the thesis proposal, and lab rotations.

All students should be aware, however, that preliminary thesis supervisors may require further coursework be undertaken as a prerequisite of accepting students into their unit for thesis research. Likewise, the Dean of Graduate School, the Thesis Committee or the Curriculum and Examinations Committee may require students undertake further coursework when deemed necessary.

All credit requirements must be submitted prior to the end of 2nd term of 5th year of enrolment.

Details regarding each element of the OIST curriculum, including completion requirements and time frames, may be found on the relevant Graduate School web page.

4.1        Extension of Due Date

Any extension of due date of any OIST curriculum requirement requires submission to the Graduate School of a “Request for Extension of Submission Due Date” request form.  Note that submission of an extension request does not guarantee approval, so requests should be submitted in a timely manner.

4.2         Elective Coursework Requirements

Elective coursework is divided into basic and advanced courses.  Elective courses may have prerequisite requirements.  Students develop an individualized course of studies in discussion with the Mentor assigned to them following enrollment.  The number of credits assigned to each course is stipulated in the Course Catalogue.

It is highly recommended and expected that elective coursework be completed within 2 years to allow focus on thesis research (following successful examination of the thesis proposal).

It is advised that students take no more than two Basic or Advanced Courses per term, in order to leave time for independent studies, reading, and research work during Rotations.

An upper limit of 50% of OIST elective course credit requirements may come from external course credit transfer.  Students should note that this limit is cumulative, so restricts the availability to subsequently also count credit from external courses, including external workshops or online courses, undertaken while at OIST.

4.2.1 Credit Transfer Policy

On approval of the Graduate School, incoming students may request credit transfer under the following conditions:

i) credit transfer may only occur from graduate level courses (Masters or Doctorate)

ii) courses for which credit transfer is sought must be STEM-related courses

iii) courses for which credit transfer is sought must not have been credited to another completed and conferred degree

iv) the student must be able to provide supporting information as required by the Graduate School for the purpose of course equivalence analysis

Transfer credits are calculated according to the following equivalence formula:

One (1) OIST credit for every 20 hours face-to-face instruction, to an upper limit of 2 credits per course, with no fractional credits allowed.

4.2.2      Course Enrollment, Change and Withdrawal

4.2.2.1 Course Enrollment

Enrollment into any course must be completed by the day before the course begins, and formal withdrawal from a course must be received by the Graduate School by the end of the teaching term.

4.2.2.2 Course Change

Course changes require endorsement of the Mentor, and must be received by the Graduate School by the end of the first calendar month of term.  Course changes in the current term require the approval of the Course Coordinator.

4.2.2.3 Course Withdrawal

Course withdrawals require endorsement of the Mentor.

To withdraw from a course with no result recorded, formal withdrawal must be received by the Graduate School by the end of the first calendar month of term.

To withdraw with “W” (Withdraw) result recorded, formal withdrawal must be received by the Graduate School by the end of the second calendar month of term.

To withdraw with “WF” (Withdraw – Fail) result, formal withdrawal must be received by the Graduate School before the end of the teaching term.

Where formal withdrawal from a course is not received by the Graduate School by the end of the teaching term, an “F” (Fail) result will be recorded.

Repetition of courses on more than two occasions requires the permission of the Course Coordinator.

4.2.3      Academic Transcript

Internal to OIST, courses repeated show in each term of enrollment with the respective grade received in that term (i.e. where an “F” grade is received, the academic record will show this in the term it is received; where the course is repeated later, the academic record will show the subsequent grade in the term it is received).

Transcripts provided for external use will however show only the highest grade achieved, in the term that the grade was received.

4.3       Mandatory Requirements (Professional and Career Development, Thesis Proposal and Lab Rotations)

The Professional and Career Development program, submission of a thesis proposal, and lab rotations form the mandatory element of the OIST curriculum.  Details regarding each mandatory element, including completion requirements and time frames, may be found on the relevant Graduate School web page.

4.3.1      Professional and Career Development

Professional and Career Development courses (I & II) are mandatory, credit-bearing elements of the OIST curriculum, and are designed to develop essential knowledge, experience, and competencies for successful completion of the graduate program, and to prepare the graduate for future careers in academia, industry, or entrepreneurship.

PCD I is prerequisite to advancement to PCD II.  Each course is worth 2 credits.

4.3.2      Thesis Proposal

A thesis proposal must be submitted for examination.  Successful completion of the examination process is worth 3 credits.

4.3.3      Lab Rotations

Rotations form a major part of the student’s work in the first year of the graduate program.  In each rotation, the student will spend one term undertaking a specific project and will then move on to a different research unit.  The Rotations provide a variety of experience in different laboratories that will broaden the student’s understanding of different disciplines, techniques, and ways of scientific thinking.  Rotations may include theoretical work or modeling, as well as laboratory benchwork. 

Importantly, lab rotations are intended to help the student select the most appropriate research unit and research question for their thesis research. 

Three Lab Rotations are mandated (including one out-of-field), with a total value of 3 credits for completion of all three.  Following Article 21-3 of “Standards for Establishment of Universities (大学設置基準)”, credits for Lab Rotations are awarded following evaluation. 

With approval of the Dean of Graduate School, prior research experience may be considered as one in-field lab rotation on equivalent completion of assignments required for this course.

Students nominate lab rotations following discussion with their Mentor.  As units may only accept 2 students for lab rotations at any time, student nominations should be in order of preference.  Placement cannot be guaranteed, but the Graduate School will always try to accommodate these preferences.

4.3.3.1      Research Internship - Lab Rotation Equivalency

Research internships of no less than four months duration, and which conform to all Lab Rotation requirements, may be considered for lab rotation equivalency.

All lab rotation requirements must be completed while the research intern is at OIST.

For Successful applicants to the OIST PhD program who enroll within twelve (12) months after the completion of research internship, the research experience may be considered as in-field lab rotation upon completion of the assignments required for the Lab Rotation.  

4.3.4     Fourth Lab Rotation

When unable to secure a preliminary thesis supervisor after three lab rotations, with permission of the Graduate School a fourth, and final, lab rotation may be accommodated on exceptional grounds.  Approval will only be granted where there is a high probability that the student may be accepted into the fourth rotation's unit as a research student at the conclusion of the rotation. 

Students are encouraged to discuss the matter with the proposed lab rotation supervisor beforehand.   The Graduate School, prior to approval of a fourth rotation, may consult with the lab rotation supervisor to discuss the matter.

Note that a fourth rotation serves solely as a last chance to secure unit placement and is not for credit.  Students’ acceptance to the thesis lab must be confirmed with the Graduate School by the thesis supervisor by the end of the third month of the rotation at the absolute latest.  This is to allow time for exiting procedures should it be necessary for the student to cease enrolment.

4.4         Course Assessment

Each course is assessed as specified in the course catalogue.  Assessment may be by means of written, practical, or oral test, or by continuous assessment, or by any combination of the above.

A student who is unable to complete an assessment item due to unforeseeable circumstances may be permitted by the Dean of the Graduate School to complete a supplementary assessment.  In such cases an application for supplementary assessment must be submitted within 48 hours of the assessment.

4.5         Appointment of Thesis Committee

All students are required to have a Thesis Committee, irrespective of the seniority of the Thesis Supervisor, to provide oversight of the thesis research supervision.  The Thesis Committee is comprised of the Thesis Supervisor, the Mentor, and the Co-supervisor or the Third Thesis Committee Member, selected from among OIST faculty members by the student in consultation with the Thesis Supervisor.  If the Co-supervisor is selected from faculty members external to OIST, an additional Thesis Committee member also needs to be selected from among OIST faculty members.  The student is responsible for nominating the Thesis Supervisor and may suggest names for the other committee members.  The members of the Thesis Committee must be nominated and approved before appointment of the Examination Panel for the thesis proposal.

Thesis Supervisors must be full-time faculty members.  In special circumstances External Faculty may be appointed as primary Thesis Supervisor, but in most cases these faculty members may only be appointed as Co-supervisor or as a Thesis Committee member.  Any exception to the above must be approved by the Dean of the Graduate School.  Faculty external to the university may be Co-supervisors provided an institutional agreement exists with the university of the external faculty member.

4.5.1      Process for Approval of Thesis Supervisor/s and Thesis Committee Members

In consultation with the intended Thesis Supervisor and Mentor, the student completes and submits the form for Preliminary Thesis Supervisor Nomination to the Graduate School.  Note that if a prospective thesis supervisor has less than four years remaining until retirement, students must also concurrently secure an internal co-supervisor.  Following the retirement of the initial thesis supervisor, the internal co-supervisor will become supervisor and take on financial and academic responsibility for the student.

Later, in consultation with the intended Thesis Supervisor, Mentor and prospective members of the Thesis Committee, the student completes and submits the form for nominating Thesis Committee members Confirmation of Third Committee Member or Co-supervisor.

The Thesis Supervisor and Thesis Committee members for each student are formally appointed by the Dean of the Graduate School, with advice from the Academic Affairs Section. If the proposed Thesis Supervisor is the same person as the Mentor, a new Mentor will be appointed by the Dean of the Graduate School to avoid any conflict of interest.

4.5.1.1      Student/Supervisor Mutual Expectations on Joining the Thesis Research Unit

To best support both students and faculty from the beginning of thesis research to successful graduation, the following policy and procedure has been developed to ensure mutual expectations are discussed before joining a thesis research lab. 

Doctoral research involves a lot of time, hard work, and importantly, development and maintenance of the supervisor/student relationship.  Shared research interests are of course important, but experience has shown that having a candid discussion about other relevant matters (for example, supervision style, communication, or remedial knowledge that may be required) before entering the lab can help avoid possible future misunderstandings and greatly improve the chances of successful completion. 

In line with Graduate School Policy “Student Responsibilities and Expectations” (https://groups.oist.jp/grad/student-responsibilities-and-expectations) and Academic Policy 4.5.2 “Preliminary Thesis Supervision” (https://groups.oist.jp/grad/academic-program-policies), the following agreement assists students and preliminary thesis supervisors come to a mutual understanding of expectations on joining a thesis research unit.   

Following a discussion of the items within (and any other relevant matters), the agreement is formalized and signed only by mutual agreement.  When mutual understanding cannot be reached, students will not be able to join the unit. 

In line with Academic Program Policy “4. OIST Curriculum Requirements” (https://groups.oist.jp/grad/academic-program-policies), when the supervisor deems it necessary that the student must first complete further study to conduct thesis research in the unit, this will be noted and a study plan developed.  Further study may consist of coursework, Independent Study, External Study and Research, or any combination thereof, and must be tailored toward the specific aims of the student’s proposed research.  If assessment of this further study is required, how this will be done will be noted in the agreement, including a timeframe of when assessment will take place.  

Assessment must happen prior to submission of the thesis proposal.  Faculty must be aware that only the further study noted in the agreement may be used to assess whether a student has reached the required minimum level of learning to remain in the unit (pending successful completion of the thesis proposal and examination process and continuing satisfactory academic progress thereafter). 

Students, in signing this agreement, bear responsibility for successfully meeting any noted requirements.  Students should be aware that non-compliance, or failing to meet these requirements, may result in the supervisor retracting their offer of thesis supervision.  As thesis supervision is a mandatory requirement following lab rotations, this may lead to discontinuation of enrollment. 

Both supervisor and student, in signing this agreement, agree to always act in good faith.  Thesis subject and research plan may change or evolve over the development of the thesis proposal, and in most cases no amendment to this agreement will be necessary.  If, however, any amendment to this agreement is deemed necessary, this must be made in a timely manner, and only by documented mutual agreement.  If deemed necessary by either party, any discussion of amendment may be attended by members of the student’s Thesis Committee. 

Finally, in all cases students should remain aware that successfully passing the thesis proposal examination remains their responsibility.  Compliance with the agreement should assist students in preparation for their thesis proposal examination but does not guarantee success during examination.  

“What if these mutual expectations are not met?” 

Graduate School encourages the supervisor and student to continue discussing their mutual expectations after the initial agreement because their situation will likely change. Both parties should bring up their concerns in these discussions if they feel their expectations are not met.  Graduate School is prepared to support both student and faculty should our assistance be requested. 
In an unfortunate case where the supervisor determines that the student has not met the expectations after reasonable attempts of communication, the following outcomes are possible.  

Cessation of preliminary supervision 

When students have not met the terms of the agreement, preliminary supervision may cease after the following:  

i. An email stating the supervisor seeks to cease supervision, including the reasons for this decision, delivered to the student (and Cced to the student’s standing members of their Thesis Committee and the Graduate School) 

ii. As soon as possible following delivery of the above email, a meeting is held in good faith between the student, standing members of the student’s Thesis Committee, and a representative of the Graduate School (for administrative reference), at least one calendar month prior to the date of proposed cessation, aimed at any possible resolution that may allow the student to remain in the unit 

iii. When the decision on cessation of supervision is final, the supervisor agrees to financially support and allow the student to remain in the unit to finalize any continuing project(s) to the date of cessation.   

Immediate repercussions of notification of possible cessation of preliminary supervision  

Students should be aware that from 2nd year of enrollment (but for those completing a 4th lab rotation) all enrolled students are required to have a thesis supervisor and placement within a research unit.  When notified that the thesis supervisor seeks to cease preliminary supervision, students are recommended to submit a Notice to Vacate Property as housing is contracted from a vendor external to OIST and cancellation of this contract requires thirty (30) days’ notice (forty (40) days’ notice for off-campus housing).  Note that where the student is able to secure thesis supervision in another unit within this period, the notice of vacation may be retracted. 
 

4.5.2      Preliminary Thesis Supervision

Status as a thesis research student in a unit is confirmed only on successfully passing the thesis proposal examination.  On receipt of a “Pass” grade, status will be automatically noted by the Graduate School.  Until that time, placement in a thesis research lab is on a preliminary basis only, and the supervisor is known as “Preliminary Thesis Supervisor”.

During writing of the thesis proposal, and through the subsequent thesis proposal examination process, students must fulfil all requirements of the Preliminary Thesis Supervisor, including lab instruction, development of the research question(s), coursework, and any remedial study required (all of which must be pertinent to the student’s thesis proposal and future research).

4.6.      External Study and Research

Students may take courses or conduct research external to OIST under the following conditions.

Following completion of lab rotations, a student may study off-campus while taking approved courses at other graduate schools or research institutions outside OIST.  Extra costs associated with External Study and Research (for example, accommodation or transportation fees) are financially supported by the Unit.

A student may conduct thesis research outside OIST only at a partner institution with which the University has entered into a formal agreement facilitated by the Graduate School.  Any period of off-campus research granted shall be counted towards the student’s enrollment.  The minimum period of external study or research allowed is one calendar month. 

Conferences, fieldwork, summer school and workshop attendance outside OIST are not normally considered as External Study and Research, but as business trips.

All periods of External Study and Research, irrespective of purpose, must be recognized by the Curriculum and Examinations Committee and approved by the Graduate School and the supervisor.  Students and faculty should be aware that concluding a formal agreement may take a sizeable amount of time, so this process should be initiated as soon as possible.

 

5.          Thesis Proposal and Examination

The PhD thesis proposal is the student’s plan for their thesis research.  The thesis proposal must be the student’s independent work.   The student is required to make an original contribution to the development of the research question, design of the research, and review of the literature.  While developing the proposal the student is expected to discuss the intended research with the thesis supervisor.  The supervisor should advise the student on what is possible in the research unit, and discuss the scientific questions, the relevant existing work, and the research design and methods.  

Students must write the thesis proposal in their own words.  In referring to the work of others correct citation and attribution of sources is essential.  Plagiarism by copying or paraphrasing is strictly forbidden, and if established may lead to a fail result without further examination.

The student’s supervisor and proposed Thesis Committee must read the proposal before it is submitted.  The student’s Thesis Committee may give feedback on the proposal and allow the student to make necessary revisions before submission.  When satisfied that the plan is achievable and that the research goals are appropriate, the supervisor and committee members indicate formal agreement by signing the submission endorsement.  The proposal is then submitted for examination. The student must defend the proposal in an oral examination. 

5.1         What constitutes a well-written Thesis Proposal? 

A well-written thesis proposal presents a research question that is formulated as a testable hypothesis.  Students must be able to define the kind of research they are proposing as a clear hypothesis and present the kind of experimentation that can address this question definitively.  Students should limit the scope of the question they aim to answer to what is achievable within the time available (approximately two years).  It is better to propose too little, rather than too much, as further research can always be undertaken if time allows.  The majority of proposals examined in the past have been required to undergo considerable reduction in scope following the examination. 

The introduction should cover the relevant literature adequately but need not be exhaustive if the literature is vast.  All important papers at least should be cited.  Students must be able to demonstrate that they are aware of both the history and the current concerns in their suggested area of research.  Students should be able to discuss what is not known, and how their research will contribute to the body of knowledge in a meaningful way.  A hypothesis should arise from the student’s analysis of what is missing and be stated clearly as one or two aims.  It is advisable to limit investigation to “something new with existing techniques”, or “a new technique with something already in existence”, but not a combination of the two. 

Proposed experiments should have the statistical power to adequately resolve the signal differences necessary to prove or disprove the thesis question.  The number of experiments necessary to adequately resolve the question must be considered and addressed in the research plan.  Experiments should not depend on the purchase of additional capital equipment, and this should be carefully discussed with the supervisor.  Students should be able to demonstrate that they can perform the desired experimental techniques and that the experiments are suited to the task.  Time-permitting, any pilot experiments and their results should be included. 

A final aspect is that of risk-management.  It is important to consider how the project may be adapted within the relevant time-constraints if all does not proceed as planned. 

The above may not necessarily apply to students pursuing research in theoretical physics or mathematics.  Nonetheless, similar clarity in stating aims, and attention to using appropriate methods, should be presented. 

The research plan should aim to finish experiments well before the end of the fifth year of enrollment (it is advisable that these be finalized by the end of the fourth year of enrollment), to allow submission of the thesis on time.  The thesis is to be submitted by the end of the second term, fifth year of enrollment.  Examinations will occur during the final term of a student’s five-year enrollment period. 

5.2         Content of the Thesis Proposal

It is part of the student's training in research to prepare a concise, rigorous, and scholarly thesis proposal, and present it in the correct format.  There is no strict length requirement for the thesis proposal.  It is anticipated that most students will need 8,000-10,000 words to adequately explain the motivation and aims of their project, review the relevant literature, and describe progress to date.  Concise proposals are however encouraged, and a proposal of 5,000 words, which covered all these points, would be acceptable. The proposal should contain the following sections: 

Front page: Students are to utilize the template provided by the Graduate School. This includes the name and logo of the OIST Graduate University, the words “PhD Thesis Proposal”, the title of the thesis proposal, the names of the student and primary supervisor (and co-supervisor, if applicable), and the date of submission.

Abstract:  An abstract should be limited to as few words as necessary; and should always be less than one page in length.  Students should be aware that many online referencing systems allow for only the first 200 words to be included.  No figures or references should be included.  Students should avoid technical and methodology details where possible.

Introduction and Literature Review: This should include a statement of the problem, the overall aims, and the background to the research including a review of relevant existing work.  The literature review should be a concise, scholarly review of the literature explaining the background to the proposed research. The review should provide the context for the aims of the proposed research in relation to existing work on the topic.

Research Plan:  This should begin with the specific aims of the research and provide a concrete plan for completion of the research including the design and methods. This section should include an explanation of how the methods will address the aims and the significance of the results for the field.  A completion timeline must be detailed in this section (for example, a GANNT chart).  This is to aid in the student’s time management over the course of their research, and further to assist examiners in their assessment of the viability of the proposal.

Progress Report: This should be a report on the research achievements of the student in the laboratory of the proposed supervisor during preliminary thesis research.  The report should not duplicate material previously submitted for evaluation as part of a previous degree but may include work completed during rotations at OIST.  The report may include examples of results obtained with the methods proposed.  It is understood that results may not be available in projects requiring, for example, development of methods, sample preparation, or recruitment of participants, in which case other evidence of progress should be reported.

Bibliography: The bibliography should include all references cited in the text but should not include references that have not been cited.  In preparing the bibliography, students may use any of the conventional styles of referencing that include the titles of articles, such as the Harvard, Vancouver or ACS systems.  However, the style chosen must be used consistently and correctly throughout, both for in-text citations, and formatting of bibliographic entries.

Appendices: These are optional and should only be used if necessary. 

The examiners commit to read the proposal, but the Graduate School or Curriculum and Examinations Committee reserves the right to require students to rewrite excessively long, or poorly constructed, thesis proposals, without forwarding them to examiners.  The student cannot assume that the examiners will read the optional appendices.

The complete thesis proposal document must be submitted to the Graduate School by the due date as nominated by the Dean (see the Academic and Examinations Timeline).  Earlier submission may be required in order to provide the thesis proposal to the examination panel no later than four weeks (28 days) prior to the oral defense.  Only in exceptional circumstances can an extension of the due date for thesis proposal submission be granted by the Graduate School, and only on receipt of a Request for Extension of Due Date before the due date.   These requests must include documented support from the student’s supervisor.

5.2.1        Formatting Requirements of the Thesis Proposal

Page size: Theses are to be formatted to A4 page size.

Margins: The left margin should be 3 cm.  Top, right, and bottom margins should be 2.5 cm.

Spacing: Spacing should be 1.5 line spaced for examination and single spacing for final submission.

Justification: The main body of text left-right justified.  Titles should be left-justified.  Equation numbers should be right justified.

Pagination: Preliminary pages, ending before the main body of text, may be numbered sequentially using roman numerals.  The main body of text, beginning with the first page of the introduction, must be numbered sequentially, including figure pages and blank pages, starting at page number 1 for the first page of the introduction.  Arabic numerals are to be used.

Font: Times New Roman, 12-point font should be used for all main body text.  For graph legends, titles, image annotations, etc., Arial, Helvetica or Calibri, 10-point font, should be used for presentation clarity.  For headings, any font or size may be used for presentation and design considerations.

Equations: Equations are considered part of the main text.  As such, they should be formatted consistently throughout the thesis proposal (or thesis), following the advice of the Thesis Supervisor.  Equations should be numbered to the right-hand margin.

Spelling: American spelling.

Colors: Color may be used in images and charts where necessary to enhance comprehension, but not for normal text or headings.  The combination of red and green for binary images should be avoided to assist those who have difficulty in discerning hues.  All text should be in black unless color-coding is necessary for meaning or contrast.

Figures: Figures should appear as close as possible to the first mention of them in the text.  All figures must be referred to in the text by either a parenthetical mark-up (Figure 1.2), or phrasing such as “Sequencing data, shown in Figure 1.2, shows that…”.  A parenthetical mention, but not an in-text mention, may be abbreviated as (Fig. 1.2).  The number of the chapter should be part of the figure number.

Figures must be accompanied by a caption that describes the material cleanly and succinctly.  Figure captions may start with a brief title in bold, which can then be referenced in the list of figures.

As a general rule, figures should not have captions that run across pages.  If a figure and its caption will be larger than one page, rewriting should be considered, or a reorganization of the figure.  If this cannot be avoided, the figure caption should continue on the immediate next page, with a reference comment at the start of the text to the fact that it is a continuation.  No other main body text should then appear on that page.

When possible or applicable, automatic placement of figures by latex is encouraged, but should be checked by the author.

Tables: All tables should be referred to in the text by number (for example, “Table 3.1 describes all particles found in…”).  Tables may be printed in landscape rather than portrait orientation but must be printed on a separate page with continuing and sequential pagination.  Tables may extend for more than one page but should then have the table header row repeated on each page.  Arial, Helvetica or Calibri, 10-point font, should be used for tables.  Tables should have a heading and may have a caption.  The number of the chapter should be part of the table number.

Images: Images are vital to presentation of scientific data.  Textual annotations must be correctly labelled, and legends, when used, must be clear and legible.  Small symbols should be used on charts for data points.  Axis marks and axis labels should be large enough to be read clearly.  All white space should be used where possible.  Headings for charts and captions explaining the data within should be meaningful.  Students must be aware of expected standards covering image manipulation and the standard practice for image presentation within their field and adhere to it.  Excessive density, contrast, and hue manipulation of photographic images should be avoided.  Where extensive manipulation of images is required for data extraction or analysis, this must be clearly explained in the description of methodology, and explicitly in the caption for each figure.

Word count/Length: As a general rule, thesis proposals should be no longer than 30 pages in length.  No minimum word count is imposed on OIST theses.  However, as with the thesis proposal, students must be concise in language and succinct in expression.  The average length of a PhD thesis will vary between fields and between authors, but typical PhD theses are 100-400 pages in length (20,000-80,000 words of main body text).

Citations: All papers cited in the thesis must be referenced in a style relevant to the student’s field.  All references must include the full title, authors, reference location and the year of publication, all in the same style for all references.  Citation style must be consistent throughout the thesis.  Reference manager software, such as Endnote, or BibTex which offers similar functionality with LaTeX, may be used.

Editing: The thesis proposal (and thesis) must be entirely the work of the student.  Minimal editing may be provided by the Thesis Supervisor(s) or peers, but only as a review of initial drafts.  Assistance should not be sought from OIST internal or paid external editing services unless directed to do so by the Dean of Graduate School in revision stages.

5.3         Thesis Proposal Examination

5.3.1      Examination Panel

The Examination Panel for the thesis proposal is comprised of three members: an External Examiner, an Internal Examiner, and a Chair appointed by the Curriculum and Examinations Committee. The Examination Panel will conduct an oral examination, up to three (3) hours in length, that will include a defense of the thesis proposal.

The Examination Panel will include an External Examiner who is expert in the field of the proposed thesis, has graduated at least one doctoral student, and is external to OIST.  The Curriculum and Examinations Committee appoints the External Examiner, taking into account nominations provided by the proposed Thesis Supervisor.  Similar conflict of interest precautions applies as outlined below.  The CEC may alternatively appoint an examiner who has not been nominated by the Supervisor.  The CEC is responsible for determining if the nominated examiner is expert in the field of the proposed thesis research.

The Examination Panel will also include an Internal Examiner chosen from OIST faculty members, who is nominated by the proposed Thesis Supervisor and appointed by the Curriculum and Examinations Committee. 

An OIST faculty member with knowledge of OIST standards and regulations concerning thesis proposal examinations is appointed by the Curriculum and Examinations Committee and will serve as chair of the Examination Panel. The Examination Panel will not include the proposed Thesis Supervisor or the student’s Mentor.  The Thesis Supervisor (and/or Co-Supervisor) only may attend the oral examination as an observer without speaking rights. 

5.3.2      Conduct of the Examination

Examinations are conducted online via video conference. If an examiner is on site for another purpose, they may attend the examination in person.

The only research material normally permitted in the examination room is the thesis proposal itself.  Additional material, including additional results developed since the thesis proposal was submitted, may be permitted provided they are supplied to the Chair of the examination at least one week in advance, and the Chair agrees to their inclusion.

After the summary, the Chairperson invites the External Examiner to examine the student.  The Internal Examiner may follow the External Examiner or, as appropriate, join the discussion with the student.  As the expert in the field of the thesis proposal, the External Examiner is expected to play the principal role in the examination.

It is expected that the examination will comprise a balance of roughly equal parts: (1) examination of fundamental knowledge in the field or fields of study relevant to the thesis topic, and (2) defense of the thesis proposal.

In (1), the student is expected to demonstrate adequate fundamental knowledge in the field or fields of study relevant to the thesis topic, and the ability to organize, apply and convey that knowledge effectively.

In the defense of the thesis proposal (2), the student is expected to demonstrate the necessary advanced knowledge and understanding to undertake the proposed thesis research and show their original and independent contribution to the proposal and the research question.  The student is further expected to demonstrate that the timeline for completion is realistic within the normal term of enrollment at OIST (5 years of enrollment in total).

In the conduct of the examination, it is envisaged that (2) will flow naturally from (1). A rigid division into parts is not necessary and the balance of time spent on each part, while nominally equal, may be varied at the discretion of the examiners.

The examination shall not continue for more than three (3) hours maximum, but may be concluded if the examiners are satisfied that they have sufficiently examined the student and are able to make a recommendation. The Chairperson formally concludes the examination when the allowed time has elapsed, or the examiners have indicated they have no further questions.

After the examination, the External Examiner and Internal Examiner independently provide written recommendations on the examination result to the Graduate School within one week of the examination.  The Graduate School in turn forwards these to the Chair.  After perusing the examiner recommendations, the Chair provides their own recommendation on examination result to the Graduate School, and to the Curriculum and Examinations Committee as required. 

The examiners recommendation must include one of the following recommended examination results listed below:

ⅰ) Pass.  The examiners recommend that the student be advanced to candidacy.

ⅱ) Pass, minor revisions required.  The thesis proposal may be accepted pending minor revisions.  No re-examination is required.  The Examiner’s recommendation should itemize the deficiencies of the thesis proposal that need to be addressed in the revisions, and any deficiencies in the scope and depth of the student’s knowledge that require remediation.

ⅲ) Major revisions required.  This outcome is possible only if the thesis proposal is not acceptable in its present form but could be acceptable pending major revisions.  The Examiner’s recommendation should itemize the deficiencies of the thesis proposal that need to be addressed in the revisions, and any deficiencies in the scope and depth of the student’s knowledge that require remediation.  Reexamination may or may not be required.

ⅳ) Fail. This is the outcome when academic preparation is insufficient, or the thesis proposal is not suitable for re-examination, or the thesis proposal has not met the required standard on re-examination.  No re-examination is allowed.

For further information please refer to the “Procedure and Responsibilities of the Chair of Thesis Proposal Examinations” found on the Graduate School website.

5.3.2.1      Re-examination of the Thesis Proposal

Any re-examination required under any circumstances will in principle be on a “Pass/Fail” basis.

Any re-submission is to be accompanied by a letter detailing the revisions made, and identifying where within the document these revisions can be found.

5.3.3      Confirmation of Result of Thesis Proposal Examination

On receipt of the examiners’ recommendations, the Chair of the examination, as the representative of the Curriculum and Examinations Committee, makes their own recommendation. 

When the Chair’s recommendation endorses the result of the examiners’ recommendations, and no objection has been raised, the result is released to the student and the Thesis Committee, and the result reported to the Curriculum and Examinations Committee.

When the Chair’s recommendation does not endorse the result of the examiners’ recommendations, the result is withheld and discussed by the Curriculum and Examinations Committee, which forwards its recommendation to the Dean of Graduate School.  The result is then released to the student and the Thesis Committee.

Examination result notifications include the recommendations of the examiners and Chair of the examination.  If revisions are required, a timeline for their completion is described.  Revisions must be endorsed by the Thesis Supervisor (but endorsement by the internal or external examiner may also be required as described in the notification). Once revisions have been endorsed, the student’s progression to thesis research is ratified at the next available meeting of the Curriculum and Examinations Committee.

 

6.          The OIST PhD Thesis

The PhD degree is conferred by the University in recognition of completion by the student of original research that makes a significant contribution to scientific knowledge.  The degree is not awarded for completion of certain courses or a fixed period of enrollment, or for directed work as a technician.  The work for the degree consists of original research and systematic studies that advance knowledge, conducted by the student with an appropriate degree of independence.  In addition, the candidate must demonstrate the ability to communicate the results of their research and scholarship effectively in both oral and written English.  The student must present their work in a thesis and defend it in an oral examination.  A student may not submit for examination work that has been included in a thesis or dissertation that has been previously submitted towards a degree qualification.

6.1         Thesis Requirements

6.1.1      Thesis by Dissertation

The thesis must present original research that makes a significant contribution to scientific knowledge. The thesis must form a coherent narrative that includes a statement of the problem, a scholarly review of the relevant literature, and must present, in detail, the methods, results, discussion and conclusions of the research.  The thesis must be formatted in chapters and submitted according to the OIST guidelines on the Preparation and Submission of the OIST PhD Thesis.  

Candidates are strongly advised to publish peer-reviewed articles in international journals based on their thesis work in a timely fashion and preferably before submitting the thesis.  Such publication of thesis research is evidence of a significant scientific contribution that may be taken into account by thesis examiners, and is essential for future career prospects.

When papers based on work completed as part of the PhD thesis are submitted, are in press, or in print, it may be possible to modify and include material from them as chapters in the thesis, providing that the thesis as a whole presents a coherent account of the research.

6.1.2      Thesis by Publication

Thesis by Publication allows students to collate their published research papers, and with complementary explanatory material, submit these in thesis format for examination.

Thesis by Publication avoids rewriting of material which the student may no longer hold copyright over once it has been published.  Although most journal companies do allow reuse of material published in their journals for the purpose of a thesis, some impose significant restrictions on republication.  Students must be aware of and abide by any such restrictions when considering the Thesis by Publication option.

To submit for examination under the Thesis by Publication option, a thesis on a single topic or line of research should be written containing an overall introduction and literature review, a list of published papers that are to be considered for the thesis, and a discussion of results and conclusions.  The thesis will thus be examined as a single, coherent work of research.

Suitable papers for inclusion as part of a Thesis by Publication are defined as “published peer-reviewed articles”, not including abstract-only publications, to which the student has made a significant contribution.

Diagrams/tables from the constituent papers may be included in the written thesis, but the text of the thesis must be the student’s own original work.  The thesis may also contain methods, results, data, and discussion not included in the published papers.

Papers published over several years will need to be set in perspective and tied into the narrative in the discussion. The discussion should include a consideration of the context and impact of each of the constituent papers, and a reflection of the development of the research as a result.  How did these papers advance the field or contribute to the subsequent research path?

Where published papers have been co-authored, the student must explicitly identify which work was their own contribution.  Examiners will be directed to consider whether the amount of work completed by the student is sufficient to merit award of the OIST PhD. 

For examination purposes, copies of the constituent papers will be distributed to examiners with the thesis.  For final publication in the OIST repository, only the final version of the thesis with links to the constituent papers is published.

6.2.        Preparation and Submission of the OIST PhD Thesis

The guidelines below set out the organization and formatting requirements of the OIST PhD thesis, in order to assist students in the preparation of theses for submission.

Plagiarism and Fraud: Students are reminded that they must take all necessary precautions to avoid plagiarism and fraudulent misrepresentation of data.  The Graduate School conducts plagiarism checks on all submitted theses, and may require rewriting if present.  When submitting a thesis by dissertation, students should avoid self-plagiarism through rewriting earlier published work and/or self-citation.

Reproducibility: OIST is committed to openness in science.  A cornerstone of this philosophy is reproducibility.  Your thesis should present all data and methods necessary to allow complete repetition of the experiments and their results, and to allow expert review of your analysis of data.  Accordingly, you must ensure that your methods are comprehensive, and that your data sets and code are available for subsequent review by lodging them in the OIST Institutional Repository or some other data repository or database, as appropriate.

Inclusion of Published Material: In some cases, inclusion of published material as chapters is desirable.  Normally, however, when published material is included in the thesis, it should be modified in order to remove redundancy and achieve a coherent narrative.  It is essential to indicate clearly any portion of the thesis that duplicates parts of articles that were previously published by the candidate.  The candidate must cite the article and indicate any parts of a section or chapter of the thesis that depend on the previously published article.  This does not apply to previous documents such as thesis proposals and reports written as part of the candidate’s research.

An appropriate level of independence on the part of the student is expected.  If parts of the thesis are based on published work under joint authorship, the supervisor should provide a statement about the extent to which this is the candidate’s own work as part of the standard supervisor declaration.

When including material from publications in a thesis, students should be aware of the copyright policies of journals.  It is recommended that students request journals to vary their normal copyright agreements to allow material from an article to be included in a thesis (as the thesis will be publicly available through the University’s library).  If, for copyright reasons, material from previously published papers may not be included in the electronically published thesis, the electronically published thesis may cite papers that are already published.

6.2.1      Thesis by dissertation format

Title Page: This page is the first printed page.

Title: Select a descriptive and unique title that clearly communicates your research.  Avoid brief or misleading titles.  The title will be displayed on your graduation testamur.  The title should be unique within OIST, to distinguish your thesis from those of others working on similar subject.

Declaration of Original Authorship: Students must provide a signed declaration that the thesis is their own work and is original.

Abstract: An abstract should be limited to as few words as necessary; and should always be less than one page in length.  Students should be aware that many online referencing systems allow for only the first 200 words to be included.  No figures or references should be included.  Students should avoid technical and methodology details where possible.

Acknowledgements: Student should acknowledge assistance received in any of the following areas:

ⅰ) research design
ⅱ) research execution
ⅲ) data analysis
ⅳ) data or research interpretation
ⅴ) writing, proofreading, or copyediting of the manuscript

Co-authorship: Co-authorship is not allowed in an OIST PhD thesis.  All research and analysis is to be the student’s own work.  Where co-authors have contributed to papers arising from the research, this data should not be included unless essential to the scientific narrative.  When included, full disclosure of the contribution is required.  Any and all work conducted by others, either internal or external to OIST, must be acknowledged.

List of Abbreviations: All abbreviations used in the thesis must be listed with their definitions.  This includes trivial and commonly used abbreviations, at your discretion, but not words that have entered general English usage (laser, for example, or DNA).  In particular, non-standard abbreviations should be presented.

Glossary: A glossary of specialized terms should be included, as necessary.

Nomenclature: Details of specialized nomenclature should be included, as necessary.

Dedication: An optional dedication may be included

Table of Contents: A table of content should include page numbers of chapters, sections, and subsections.

List of Figures and List of Tables: A list of figures (and likewise a list of tables) should be included.

Main body: The main body of text may be arranged as a single body of material, divided into subsections of Introduction (including a statement of the problem to be investigated), Methods, Results, Discussions, or, if preferred, in chapters that each deal with a smaller part of the research, each itself divided into subchapters as above.

Reference List: A complete list of all articles and books cited within the thesis, once only, at the end of the thesis.  Citations should provide the title of the reference, and list at least the first three authors (et al. format is acceptable).  Articles not cited within the thesis should not be included.

Appendices: As required.  Unlike a journal article, no data or discussion may be presented separately as unpublished supplementary documents or data.  Appendices should be used instead for material that is tangentially relevant to the thesis but does not belong in the main narrative.  If reference is needed to large volumes of data that cannot be printed (for example, an annotated genome, or a simulation including moving images), the data should be located on an OIST repository or public database and the URL of the dataset provided in the thesis.

6.2.2. Thesis by publication format

Title Page: This page is the first printed page.

Title: Select a descriptive and unique title that clearly communicates your research.  Avoid brief or misleading titles.  The title will be displayed on your graduation testamur.  The title should be unique within OIST, to distinguish your thesis from those of others working on similar subject.

Declaration of Original Authorship: Students must provide a signed declaration that the thesis is their own work and is original.

Abstract: An abstract should be limited to as few words as necessary; and should always be less than one page in length.  Students should be aware that many online referencing systems allow for only the first 200 words to be included.  No figures or references should be included.  Students should avoid technical and methodology details where possible.

Acknowledgements: Student should acknowledge assistance received in any of the following areas:

i) research design
ii) research execution
iii) data analysis
iv) data or research interpretation
v) writing, proofreading, or copyediting of the manuscript

Co-authorship: Co-authorship is not allowed in an OIST PhD thesis.  All research and analysis is to be the student’s own work.  Where co-authors have contributed to papers arising from the research, this data should not be included unless essential to the scientific narrative.  When included, full disclosure of the contribution is required.  Any and all work conducted by others, either internal or external to OIST, must be acknowledged.

List of Abbreviations: All abbreviations used in the thesis must be listed with their definitions.  This includes trivial and commonly used abbreviations, at your discretion, but not words that have entered general English usage (laser, for example, or DNA).  In particular, non-standard abbreviations should be presented.

Glossary: A glossary of specialized terms should be included, as necessary.

Nomenclature: Details of specialized nomenclature should be included, as necessary.

Dedication: An optional dedication may be included

List of Publications: List publications, including links to constituent papers, and identify your contribution to each article.

Table of Contents: A table of contents should include page numbers of chapters, sections, and subsections.

List of Figures and List of Tables: A list of figures (and likewise a list of tables) should be included.  Lists must be sequential (listing figures and tables in order of appearance in the thesis).  As with citations, these lists serve to assist the reader in efficiently locating sought after information.  As such, please note that these tables may require amendment in the post-examination final version of thesis as publications must be removed prior to submission.

Main body: The main body of text may be arranged as a single body of material, divided into subsections of Introduction (including a statement of the problem to be investigated), Methods, Results, Discussions, or, if preferred, in chapters that each deal with a smaller part of the research, each itself divided into subchapters as above.

Reference List: A complete list of all articles and books cited within the thesis, once only, at the end of the thesis.  Citations should provide the title of the reference, and list at least the first three authors (et al. format is acceptable).  Articles not cited within the thesis should not be included.

Appendices: As required.  Unlike a journal article, no data or discussion may be presented separately as unpublished supplementary documents or data.  Appendices should be used instead for material that is tangentially relevant to the thesis but does not belong in the main narrative.  If reference is needed to large volumes of data that cannot be printed (for example, an annotated genome, or a simulation including moving images), the data should be located on an OIST repository or public database, and the URL of the dataset provided in the thesis.

6.2.3      Formatting Requirements

Formatting requirements of the thesis are identical to those of the thesis proposal.

 

7.          Thesis Defense Examination and Graduation Requirements

A candidate is examined both on the written thesis and in an oral examination. The examination process is strictly confidential. The candidate must submit to the Graduate School written Notice of Intent to Submit a Thesis in accordance with the Academic and Examinations Timeline for the examination to be arranged before the proposed submission date.  Before submission of the thesis, the Graduate School must confirm that the course credits necessary for graduation have been completed.

7.1         Appointment of Thesis Examination Panel 

After receiving the Notice of Intent to Submit a Thesis, the Curriculum and Examinations Committee will appoint a Thesis Examination Panel from within and outside the University as follows:

Two Examiners, selected from two different working-countries, who have graduated at least one doctoral student each, and who are expert in the field (or part thereof) of the thesis and external to OIST.  The CEC appoints examiners taking into account nominations provided by the Thesis Supervisor.  The Thesis Supervisor is responsible for ensuring that nominated examiners meet CEC requirements.  The Academic Affairs Section of the Graduate School is responsible for checking that these requirements are met.  If the requirements are not met, the nomination shall not be submitted to the CEC, and the Thesis Supervisor shall be informed of the reason(s) for declining the examiner and asked to provide a new nomination.

The CEC may alternatively appoint an examiner who has not been nominated by the Supervisor.  The CEC is responsible for determining if the nominated examiner is expert in the field of the proposed thesis research.

A Chair selected from OIST faculty members with knowledge of OIST standards, regulations and procedures concerning PhD thesis examinations.  

7.2         Conflicts of Interest in Examinations 

The CEC will not appoint examination panel members who have or appear to have conflicts of interest.  For OIST faculty members, a conflict of interest is deemed to exist if the faculty member is involved in the supervision of the thesis research of the student, or is collaborating in the research project of the candidate.  For non-OIST faculty members a conflict of interest is deemed to exist if they: 

i) are involved in the research, 
 
ii) have current collaborations with members of the thesis laboratory, or previous collaborations in the past 5 years; 
 

iii) have had prior or ongoing contact with the Thesis Supervisor and/or Co-supervisor that may appear to compromise objectivity, such as having been in the same department as the Thesis Supervisor and/or Co-supervisor, having been a thesis or postdoctoral supervisor of the Thesis Supervisor and/or Co-supervisor (or vice versa), or having joint publications or grants with the Thesis Supervisor and/or Co-supervisor in the past 5 years; 
 
iv) have had prior contact with the student that may appear to compromise objectivity, such as having been in the same department as the student, having supervised the student in academic or project work, or having joint publications or grants with the student at any time 
 
v) will be examining consecutive students of the Thesis Supervisor and/or Co-supervisor

7.3         Examination of the Written Thesis

The two external examiners read the thesis, and separately prepare a recommendation regarding the acceptability of the thesis for a PhD and progression to oral examination from the following:

ⅰ) Pass.  I recommend the thesis be accepted as is and the student be advanced to oral examination.

ⅱ) Pass, minor revisions required.  I recommend the student be advanced to oral examination.  The thesis may be accepted pending minor revisions.  No re-examination of the written thesis is required.  The Examiner’s recommendation should itemize the deficiencies of the thesis that need to be addressed in the revisions.

ⅲ) Defer.  This outcome is possible only if the thesis is not acceptable in its present form but could be acceptable pending major revisions.  The Examiner’s recommendation should itemize the deficiencies of the thesis that need to be addressed in the revisions.  Oral examination cannot proceed until these revisions are complete and the written thesis re-examined.

ⅳ) Fail. This is the outcome when academic preparation is insufficient, or the thesis is not suitable for re-examination, or the thesis has not met the required standard on examination.  No re-examination is allowed.

The Chair of the Thesis Examination Panel reviews the recommendations and decides if the oral examination may proceed.  Where necessary, the Chair may formally seek advice related to the thesis research from other OIST faculty with relevant knowledge of the field.

Where the result is in dispute, the Chair may convene a meeting of the Thesis Examination Panel to determine a joint recommendation, or may unilaterally provide their own recommendation which is passed to the CEC along with the examiners’ individual recommendations. The CEC then provides a recommendation to the Dean of Graduate School on a final result.

7.3.1         Re-examination of the Written Thesis

Any re-examination required under any circumstances will in principle be on a “Pass/Fail” basis.

Any re-submission is to be accompanied by a letter detailing the revisions made, and identifying where within the document these revisions can be found.

7.4         Oral Examination 

The Thesis Examination Panel conducts a closed oral examination for up to two hours via video conference.  If an examiner is on site for another purpose, they may attend the examination in person.  It is a requirement that all examiners participate in the oral examination.

The Thesis Supervisor (or Co-Supervisor) may attend the oral examination, but only with the express permission of all primary participants of the examination (the student, the Chair, and the examiners).  Permission to attend is sought by the Academic Affairs Section only.  Any objection raised will mean the Thesis Supervisor (or Co-Supervisor) is unable to attend the examination.  The reason for any objection will not be disclosed.  When allowed, the Thesis Supervisor (and Co-Supervisor, as applicable) may attend only as an observer, and may not participate in the examination.

After the oral examination the examiners provide a recommendation of result from one of the following:

i) Pass.  I recommend the student pass the oral examination.

ii) Pass, minor revisions required (mandatory).  I recommend that the student pass the examination.  The thesis may be accepted pending minor revisions.  No re-examination is required.  The Examiners’ recommendations itemize the deficiencies of the thesis that need to be addressed in the revisions.

iii) Pass, minor revisions recommended (optional).  I recommend the student pass the oral examination.  Minor revisions are recommended and are detailed in the Examiner's Recommendation. These revisions are not mandatory and may be completed at the student's discretion alone.  No re-examination is required.

iv) Fail. This is the outcome when academic preparation is insufficient, or the thesis is not suitable for re-examination, or the thesis has not met the required standard on examination.  No re-examination is allowed.

The Chair, after receiving the examiners’ recommendations, will prepare their own recommendation of result, stating their recommendation chosen from the options listed above and including relevant points of discussion that contributed to the decision.

The Chair’s recommendation will be forwarded to the Dean of the Graduate School and, if required by the Chair, the Curriculum and Examinations Committee.

In the case of a “Pass” outcome, the candidate is informed by the Dean of the Graduate School and must lodge the final version of the thesis with the Graduate School.

In the case of a “Pass, minor revisions required” outcome the recommendation specifies the revisions to be made, which may be by reference to individual examiners’ reports. The Dean of the Graduate School informs the candidate of the required revisions.  After the candidate has made the revisions the Thesis Supervisor (and, when applicable, one or both examiners) approves the final version of the thesis or, if the revisions are unsatisfactory, the thesis is returned to the student for further corrections. When the final version of the thesis has been approved, the student must lodge the final version of the thesis with the Graduate School. Where revisions are optional only, the student may choose to submit as is without endorsement. Note, however, that if opting to revise, these revisions too must be endorsed by the Thesis Supervisor(s) prior to submission of the final version of the thesis.

It is strongly recommended that students remain at OIST until the final version of the thesis has been accepted and lodged with the Graduate School.

A candidate who has failed the thesis examination may lodge an appeal. The procedures for an appeal are separately stipulated.

7.5         Public Presentation 

There is no requirement for a public defense of the degree thesis as part of the examination process.  As a graduation requirement, however, and as part of their professional development, students are expected to give a final presentation of their research for the OIST community.  Examiners are asked to attend the public presentation without speaking rights and are advised that the public presentation does not form part of the examination.

7.6         Summary of Graduation Requirements

In order to graduate with the OIST doctoral degree, a candidate must have been registered as a full-time student for a minimum enrollment period stipulated in Article 35 of the University Rules and successfully met the following minimum requirements: 

ⅰ) successfully completed at least 30 credits, including all mandatory credit-bearing elements of the program,
ⅱ) published, or submitted for publication in a peer-reviewed journal, at least one article, derived from OIST-funded thesis research.
ⅲ) submitted a PhD thesis for examination,
ⅳ) have given a public presentation of their thesis research,
ⅴ) obtained a Pass outcome of the Thesis Examination

The academic record for the candidate will record the name of the Thesis Supervisor and list separately the names of the members of the Thesis Committee. 

 

8.          Student Academic Progress

The Graduate School is committed to early identification and support of students who are not meeting academic requirements, and to maintaining academic standards of students in the PhD program.

The Academic Affairs Section, on behalf of the Dean of Graduate School, monitors the academic progress of all students, including performance in lab rotations, coursework, and thesis research.

8.1         Monitoring of Academic Progress

Regarding coursework and lab rotations, grades are collated and assessed to ensure continued academic success.  Successful completion of pre-requisite coursework is also confirmed before students are allowed progression to subsequent courses.

Any “Fail” grade in any academic year will constitute lack of academic progress.

Students who are not meeting academic program requirements are alerted by the Dean of the Graduate School.  The Graduate School may require the student to meet with their Mentor to discuss and decide upon a course of action. 

Students may be required to undertake remedial action, including further coursework, as required by the Dean of Graduate School.  Mandatory courses of action may be developed in communication with the student’s Mentor or Thesis Supervisor, as appropriate.  In any case, the Mentor and Thesis Supervisor will be informed of any required course of action.

Satisfactory academic progress thus requires a level of performance in courses and rotations meeting all of the following criteria:

ⅰ) Attaining 20 credits of elective coursework with at least a “Pass” evaluation in all courses, at a rate sufficient to meet the cumulative credit requirements for graduation by thesis submission

ⅱ) completing all required rotations with at least a “Pass” evaluation

ⅲ) successfully completing all other curriculum mandatory requirements (submission of thesis proposal and Professional and Career Development I & II)

8.2         Progression to PhD Thesis Research

OIST graduate students will be eligible for PhD thesis research on submission of the thesis proposal and successfully passing the subsequent examination.

In submitting the thesis proposal for examination, students are required to have adequate fundamental knowledge in the field or fields of study relevant to the thesis topic, and to have the ability to organize, apply and convey that knowledge effectively.

The Dean of Graduate School, in confirming student’s progression to thesis research, may require remedial action or further courses of study be undertaken.  The student’s Thesis Committee will be informed of any such requirement, and confirmation from the Thesis Committee that this is completed within a prescribed timeframe may be required.

In addition to thesis proposal examination results, a report may be made to the Curriculum and Examinations Committee of students who are yet to complete their elective credit requirement, but this does not preclude students from advancement to thesis research.

8.3         Monitoring of Academic Progress in Research

From the beginning of the student’s second year of enrollment, the Thesis Supervisor takes primary responsibility for monitoring research progress of the student, assisted by the Thesis Committee.  The Mentor will continue to advise and provide support, able to act in a confidential manner in case of difficulties between the student and the Thesis Supervisor.

Satisfactory progress in research is defined by the following criteria:

i) meeting relevant milestones in accordance with the student’s Academic and Examination Timeline
ii) submission of a thesis proposal and passing the subsequent thesis proposal examination
iii) satisfactory Research Progress Reviews
completion of the PhD thesis within five years of commencing the program

In addition:

iv) successful completion of Professional and Career Development II (undertaken concurrently with thesis research)

8.4         Research Progress Review

The Research Progress Review, completed by the mid-point of a student’s academic year from year 3 of enrollment onward, serves to ensure faculty oversight of ongoing academic progress, and to provide opportunity for the student’s Thesis Committee to identify difficulties that may have arisen during the student’s research and provide assistance if necessary.

The Research Progress Review requires presentation of a Research Progress Report by the student to the Thesis Committee, with a subsequent discussion on the report and the presentation’s contents.  Thesis Committee members then submit individual reports to the Graduate School on the review, recommending that the review be considered satisfactory, and/or identifying any concerns they may have.

Ideally students will meet with the Thesis Committee as a whole, but in exceptional circumstances students may meet with members individually to accommodate one or another member’s availability.

Satisfactory progress in research is defined by the following criteria:

ⅰ) meeting relevant milestones in accordance with the student’s Academic and Examination Timeline

ⅱ) submission of a thesis proposal and passing the subsequent thesis proposal examination

ⅲ) satisfactory Research Progress Reports

ⅳ) completion of the PhD thesis within five years of commencing the program

In addition:

ⅴ) successful completion of Professional and Career Development II (undertaken concurrently with thesis research)

8.4.1         Research Progress Report

Research Progress Reports on the progress of the student’s thesis research must first be submitted to the Graduate School, who will ensure all constituent elements are included and that the report meets the requirements of the Research Progress Review.  On acceptance by the Graduate School, the report is forwarded to the student’s Thesis Committee and students are asked to organize the required meeting with their Thesis Committee and provide a presentation on the report’s contents. 

A Research Progress Report should be 1-5 pages in length, and contain the following:

i) clarification or reiteration of research goals
ii) academic progress to-date (or since last report),
iii) if applicable, identification of unforeseen difficulties that have led to a change in research direction,
iv) if applicable, how the above difficulties have been overcome,
v) an up-to-date research timeline, including an explanation of how the research timeline has changed (and any requirement of extension), if applicable
vi) leave plans, and any possible effect on research progress

8.5         Unsatisfactory Academic Progress

Unsatisfactory academic progress may be defined as failure to meet any of the criteria listed above, notwithstanding legitimate and approved extension requests.  The Dean of Graduate School may, as deemed necessary, refer any matter to the Curriculum and Examinations Committee for its assessment and recommendation of a course of action.

In the case of established unsatisfactory academic progress, the Dean of Graduate School, taking into account the recommendation of the Curriculum and Examinations Committee if deemed necessary, may decide on academic probation or discontinuation of enrollment.

8.6         Academic Probation

If a student is placed on academic probation, the Dean of Graduate School alerts the student and explains the conditions the student must meet for satisfactory academic progress.  Likewise, the Dean’s notice will stipulate any restrictions placed on the student for the duration of the academic probation.

The student’s Thesis Committee will be informed of any required course of action, and may be required to report to the Graduate School on progress (through an RPR or otherwise).  Academic probation may be lifted if the student is able to accommodate or complete any remedial course of action required by the Dean of Graduate School within a specified timeframe.

8.7         Discontinuation of Enrollment

Discontinuation may be applied if a student fails to make satisfactory academic progress.

In such cases the Dean of Graduate School may order the discontinuation of that student upon obtaining permission from the President, and with endorsement of the decision by the Curriculum and Examinations Committee.

8.8         Year 7 of Enrollment Onward (To 10 Year Limit of Enrollment)

With enrollment at OIST limited to ten years, by year seven of enrollment measures will be put in place to ensure students are able to submit their thesis, and successfully pass examination, without unnecessary delay.

Further oversight of a student’s research progress will be expected from year seven of enrollment onward in the form of termly research progress reviews, rather than an annual review.

Before beginning their seventh (and eighth and ninth, if required) year(s) of enrollment, students will be required to submit to the Graduate School an updated completion plan endorsed by their Thesis Committee.  The completion plan must include thesis submission by the end of the ninth year of enrollment at the absolute latest.

The Curriculum and Examinations Committee will be informed of all students who are in their seventh year of enrollment onwards, and the completion plan will be submitted for the Committee’s perusal.  The Curriculum and Examinations Committee may at their discretion call for further measures.

As one full year is required to ensure all permutations of the examination process may be accounted for, the student’s tenth year of enrollment is dedicated entirely to the examination process, including requisite revisions.  For this reason, if the student’s thesis is not submitted by the end of year nine of enrollment, no extension of enrollment will be offered.

 

9.          Cessation of Supervision Policy

In cases of documented and continued lack of academic progress, where demonstrable accommodation has been made by the supervisor to ensure the student has had reasonable opportunity to advance their research, and where a change of supervisor is unfeasible, supervisors (including co-supervisors, where applicable) may cease supervision of a research student.

Initiation of this policy by the supervisor requires approval of the Thesis Committee.  When implemented, if the research remains viable, the student is required to submit a completion plan with expected completion within six months.  The supervisor concurrently informs the Graduate School of the request.

On receipt, the supervisor meets with the Thesis Committee to discuss and adjust the completion plan.  The Thesis Committee then meets with the student to discuss any necessary changes and to make clear expectations of the student during the six months of the completion plan.

The Graduate School may be invited with the permission of all attendees to the above meeting but must be informed of the outcome.

The final completion plan begins with mutual understanding between the student and Thesis Committee of the outcome of the meeting and following electronic submission to the Graduate School of the completion plan by the Thesis Committee.

Funding is provided by the supervisor.  The possibility of further self-funded enrollment with access to the unit as a consequence of examination outcome is by negotiation between the student and the supervisor.

 

10.         Graduation

Conferment of Degree

On meeting OIST graduation requirements, the secretariat of the Curriculum and Examinations Committee passes to the Faculty Assembly the recommendation to award the degree.  The recommendation shall be sent electronically.  If there are no objections within three working days, the recommendation shall be considered as having been confirmed by the Faculty Assembly.  In the case that there are valid objections the matter shall be put on the agenda for the next Faculty Assembly meeting, and the student and members of the thesis committee shall be informed.  The Dean of the Graduate School shall prepare a recommendation for the Faculty Assembly after hearing the nature of the objection.

Once the Faculty Assembly has approved the recommendation, the minutes of the Faculty Assembly hold a record of the names of the students, the date of conferment, and title of the thesis. The date of conferment shall be the last calendar day of the month in which the Faculty Assembly approved. The Individual Student Record shall be updated on the 1st of the following month (or the next business day), stating that all requirements for the degree have been satisfied and the degree has been conferred. The record includes the date, the title of the thesis, the name of the Thesis Supervisor, and the names of the other members of the Thesis Committee.

At the time when the individual Student Record is updated, the student is sent a letter confirming that the degree has been conferred and that the student may receive their degree certificate at the next graduation ceremony or “in absentia”. The degree certificate is presented by the President at the graduation ceremony.  A student who chooses to graduate in absentia is provided with the degree certificate after the graduation ceremony.

When a Doctoral degree is conferred, it shall be reported to the Minister of Education, Culture, Sports, Science and Technology, and the abstract of the thesis and the result of the examination shall be publicized within 3 months following the day of the conferment of the Doctoral degree.

The entire text of the thesis related to the conferment of the Doctoral degree shall be published within one year following the day of the conferment of the Doctoral degree; provided however, that this shall not apply to the thesis published prior to the conferment of the Doctoral degree.

The student may request that the full text not be published, and instead only publish a summary of the contents of the thesis in lieu of the entire text of thesis when there is significant reason and with approval of the Supervisor.  In this case, the University will make available for inspection the entire text of the thesis in response to a request, in hard copy and on University library premises.  When necessary for intellectual property protection or other reasons, this inspection will be subject to a non-disclosure agreement.  When the Dean of the Graduate School judges that the significant reason no longer exists, the entire text of thesis related to the conferment of the Doctoral degree shall be published through the medium specified by the university.

 

11.         Professional and Career Development

11.1         Career Advice

The OIST Graduate School has a dedicated Professional and Career Development Coordinator in the Curriculum and Programs Section.  The Professional and Career Development Coordinator provides individual consulting advice, as well as help with writing curriculum vitae.

11.2         Teaching Assistantship

The OIST Graduate School, at its discretion, may offer OIST PhD students the opportunity to gain experience and develop skills   as Teaching Assistants.  Teaching Assistants may contribute to various educational activities such as:

ⅰ) assisting an OIST faculty member in the delivery of an official OIST Graduate School course.  Teaching Assistants may contribute to activities such as laboratory classes and tutorials and preparation of materials under the supervision of the faculty member.  It is expected that the OIST faculty member is present for the scheduled teaching hours to provide mentoring and quality control; this should not be used to replace faculty in teaching. Selection as a Teaching Assistant for a course is decided by the faculty member in charge of the course

ⅱ) acting as tutors in OIST International Workshops and Courses, or in preparatory or remedial courses for OIST students.  Selection is decided by the faculty member in charge of the workshop or  course

ⅲ) contributing to educational outreach activities such as open campus or school visits; with selection decided by the organizer of the outreach activity

ⅳ) assisting in educational activities at other universities, by agreement between the universities; with selection decided by the graduate school in consultation with the other university

ⅴ) assisting in other educational activities organized by the Graduate School

Teaching experience is important for an academic career. The Graduate School will keep a record of Teaching Assistant activity for each student.

Teaching Assistants are expected to prepare thoroughly for their teaching activity by reading all materials and studying any necessary background.  Preparation of material may be required. Attendance at training provided as part of Professional and Career Development courses is also expected.  Teaching Assistants will normally only be appointed after successfully completing their thesis proposal examination.

Students wishing to apply for Teaching Assistant appointments should discuss their request with the faculty member or organizer of the educational activity, and later with the Professional and Career Development Coordinator.

Service as a Teaching Assistant is unpaid as students receive financial support by other mechanisms.

 

12.        Textbook

The University recognizes that support for taught courses is an essential component of student success.  Accordingly, the Library endeavors to make available both in person and online copies of all books set as textbooks and reference books for courses. 

Books designated as textbooks and reference books will be restricted from general loan during the teaching term of the associated course. One copy will be made available to students in a Reserve Collection, to be used on a temporary basis on request, in the Library only. Any additional copies may be loaned by students of that course on a monthly basis (the standard loan period), to permit use across the class. 

Students are encouraged to purchase their own copies of textbooks as appropriate.

 

13.        Computers

OIST PhD Students will be provided with a standard laptop computer adequate for their basic needs for communication, coursework and thesis writing during their time at OIST.  Research Units are to provide for any additional computer needs as required for the students’ research during lab rotations and/or their thesis research if students’ supervisors deem it necessary. Use of the OIST IT issued computers must conform with OIST PRP Chapter 17 Information Technology and Security.

 

14.        Teaching Spaces and Resources Management

Graduate School spaces and resources will be made available for use by the OIST Community for the purpose of teaching and learning in line with the OIST Teaching Labs Facility & Resource Use Policy.

Graduate School teaching spaces are intended to support teaching and learning at OIST. Priority is given to use in official Graduate School courses and other Graduate School sponsored trainings and events.  When a space is not in use, it may be booked and used with prior approval of the Graduate School.

 

15.        Graduation Ceremony

The University holds an annual Graduation Ceremony, to which all eligible PhD graduates from the preceding year are invited. The President will present those graduates in attendance at the ceremony with their degree certificates in the presence of the assembled faculty of the University.  Graduates who choose to graduate in absentia will be mentioned at the ceremony and their certificate will be sent to them by mail.

15.1       Academic Dress

OIST official academic dress comprises a black gown with red border and white piping, together with a black velvet tam and tassel. PhD graduates of the OIST Graduate University augment the university gown and tam with a hood, presented at the graduation ceremony.  Academic dress is made available by the Graduate School for rent or purchase by faculty members, students, and graduates.  The rental fee covers cleaning and other costs, while the purchase cost reflects the actual cost of academic dress manufacture.  Graduating students may elect to rent for the graduation ceremony and purchase at a later date.  Academic dress rentals are not permitted for off-site use.

 

16.        Improvement of Education

16.1       Basic Policy of Faculty Development

The Graduate University must maintain and improve the quality of its Faculty in order to provide an outstanding education at OIST and to meet the different educational needs of each student.  The Graduate School will play an active role in the development of faculty members by implementing programs for faculty development in teaching and supervision of graduate students.

16.2       Methods

Specifically, the Graduate University will conduct the following:

16.2.1    Teaching Guidelines

The Curriculum and Programs Section of the Graduate School will create, maintain, and distribute guidelines for quality teaching to ensure uniform best-practice teaching standards are observed at OIST.

16.2.2    Student Teaching Evaluations

Students will evaluate each course at the end of the course.  The results of such evaluations will be distributed to the teacher, and will also be available to students.  The student responses to a standard subset of questions will be reported to the Office of the Dean of the Graduate School.  The Curriculum and Programs Section of the Graduate School will assist the teacher to respond appropriately to this feedback.

16.2.3    Peer Review of Teaching

Faculty members will support the development of their colleagues by participating from time to time as classroom observers, with the agreement of the teacher.  The date of such observation will be reported to the Office of the Dean of the Graduate School, and the observer will discuss their observations with the teacher in a collegial and supportive manner.

16.2.4    Teacher Training

The Curriculum and Programs Section will arrange training sessions, and workshops for faculty development from suitably qualified facilitators, in order to enhance the teaching ability of OIST Faculty members.

16.2.5    Faculty Mentoring

A mentoring system will be established so that faculty with less experience in teaching and thesis supervision can meet with more experienced faculty to receive advice and support.  As a part of this system the Thesis Committee supervising each student will include junior and senior faculty members to facilitate the transfer of skills relating to supervision of research.

The Curriculum and Programs Section will implement these methods to ensure the improvement of the education and research of the Graduate University.

 

 

Supplementary Provisions

This Academic Program Policies shall come into force from September 1, 2020.

Supplementary Provisions

This revised Academic Program Policies shall come into force from May 1, 2021.

Supplementary Provisions

This revised Academic Program Policies shall come into force from May 1, 2022.

Supplementary Provisions

This revised Academic Program Policies shall come into force from May 1, 2023.

Supplementary Provisions

This revised Academic Program Policies shall come into force from September 1, 2023.

Supplementary Provisions

This revised Academic Program Policies shall come into force from May 1, 2024.

Supplementary Provisions

This revised Academic Program Policies shall come into force from January 6, 2025.

Supplementary Provisions

This revised Academic Program Policies shall come into force from April 1, 2025.

 

Student Support Policies