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Research Thesis Requirements and Timeline

For All Master's Programs in Biological Sciences

BEFORE BEGINNING: Students who wish to do a Master's Thesis should find a research lab. In order to do a thesis, a student must work a minimum of 1 semester (although more typically 1 semester plus a summer) in a research lab before beginning their last semester in the MS program. The following steps will begin before the start of the last semester in the program and go through until the weeks leading up to completion of the degree. Students who want to have help finding a research lab should contact the program academic advisor.

The timeline is relative to graduation. Graduation is always one week after the last day of final exams in the semester of graduation. Please refer to the Academic Calendar: https://www.cmu.edu/hub/calendar/ .

Assistant Department Head of Graduate Affairs

DJ Brasier dbrasier@andrew.cmu.edu
MI 415A
412-268-1951

Step 1: Thesis Proposal

Begin at least 6 months prior to graduation. Must be completed at least 4 months prior to graduation.

  • If you are graduating in December, this means you must begin steps 1a–1d by June 1st. You must complete each by its own deadline but steps 1a–1d must all be completed by August 10th.
  • If you are graduating in May, this means you must begin by November 1st. You must complete each by its own deadline but steps 1a–1d must all be completed by January 10th.

Step 1a: Pre-Proposal Planning

If you are graduating in December, then you must begin this process by June 1st and complete it by July 1st. You must have an in person conversation with your thesis advisor no later than June 10th and you must then send an email to your thesis advisor and CC the Assistant Department Head of Graduate Affairs no later than 11:59 pm on June 11th. Any exception to this deadline requires written permssion from the thesis advisor and th Assistant Department Head of Graduate Affairs.

If you are graduating in May, then you must begin this process by November 1st and complete it by December 1st. You must have an in person conversation with your thesis advisor no later than November 10th and you must then send an email to your thesis advisor and CC the Assistant Department Head of Graduate Affairs no later than 11:59 pm on November 11th. Any exception to this deadline requires written permssion from the thesis advisor and th Assistant Department Head of Graduate Affairs.

Students meet with their planned thesis advisor at least 5 months prior to graduation (preferably 6-7 months prior to graduation).  In this meeting they should review all the thesis steps in the thesis.  If both agree that a thesis is a valuable endeavor, they should begin to work together on thesis proposal and identifying committee members.  Following the meeting, the student should e-mail dbrasier@cmu.edu and CC the advisor stating that s/he is planning to complete an honors thesis and a draft title.

NOTE: This is a separate process from research for credit. Students doing an honors thesis must complete at least 12 units of research for credit (03-699 or 06-600) during their time at CMU; this is typically done before the formal thesis proposal. In the final semester, students can also enroll in 03-700 (honors thesis research) once they have finished steps 1a-1d. (NOTE: if you are a paid research assistant in the lab, you do not register for 03-700 but you still may do the thesis and receive the research honors for thesis completion.)

Step 1b: Proposal Writing

If you are graduating in December, the proposal needs to be completed by August 11th. The completed proposal needs to be submitted to your research advisor and CC'd to dbrasier@cmu.edu no later than 11:59 pm on August 10th. If it is not completed by then, you will not be permitted to complete your thesis.

If you are graduating in May, the proposal needs to be completed by January 10th. The completed proposal needs to be submitted to your research advisor and CC'd to dbrasier@cmu.edu no later than 11:59 pm on January 11th. If it is not completed by then, you will not be permitted to complete your thesis.

Students should work with their advisor to write a 2-4 page thesis proposal document.  The proposal should demonstrate understanding of the background material, project rationale, experimental design, methods underlying the proposed project and possible outcomes.  The Thesis Proposal should have the following sections:

  • Specific Aims (1-2 aims, appox. 0.5 page). State concisely and realistically what your research is intended to accomplish and what hypotheses are to be tested.
  • Background & Significance (appox. 1 page). Briefly sketch the background to the proposal, critically evaluate existing knowledge and specifically identify the gaps that the project is intended to fill, i.e., summarize the general knowledge of the field, and identify where your questions fit in. This important section displays your knowledge and understanding of the field and its current shortcomings. What are the major unanswered questions? Include previous work done by yourself, your lab, and other labs.
  • Experimental Design and Methodologies (approx. 1 page). Discuss the experimental design and the procedures to be used to accomplish the specific aims of the project. Include potential difficulties and limitations of the proposed procedures, and alternative approaches to achieving the aims.
  • Literature Cited. References should be cited within the text by first author and year (Smith et al., 1888; Wilson and Jones, 1919) and listed at the end of the proposal in alphabetical order by first author’s last name. The page limit does not include references.

The proposal should be sent to the thesis advisor (faculty member in charge of the lab) at least 3.5 months prior to planned graduation so that the advisor can review the document before the student sends it along to the committee and to the academic advisor (step 1d).

Step 1c: Committee Make-up and Members

When you meet to talk about doing a thesis, you also need to begin working with your advisor to identify two other faculty members to be on your committee. You should start this at the same time as you start your thesis proposal (note that committee member commitment is due before the thesis proposal) . You are responsible for emailing each suggested committee member and CC'ing your research advisor in enough time to get a response from the committee members. If you aren't getting responses, work with your thesis advisor to determine if you should keep trying to contact the same people or if you should start to find other possible advisors. If the first people you contact are unavailable, then you should contact others. You must have written confirmation of a commitment to serve on your committee from two other faculty no later than one week before the deadline for completion of the thesis proposal (see the steps above and below).

 The thesis advisor will serve as the chair of the thesis committee.  At least two members of the thesis committee must be full-time faculty at Carnegie Mellon University, including at least one person who holds the rank of Tenure-Track Assistant Professor or higher in the Department of Biological Sciences; if the thesis advisor is not a tenure-track professor in Biological Sciences, then at least one other member of the committee must be.  The committee must also include representation from two departments in Carnegie Mellon University or one department in Carnegie Mellon University and one full-time faculty member from another university. 

The obligations of the committee member are as follows:

  • Respond to emails confirming they are able to evaluate your work.
  • Read your thesis proposal and provide any feedback they have on it.
  • Read your progress report (which will be in the middle of the semester) and provide any feedback they have on it.
  • Read your final written thesis document and provide any feedback they have on it.
  • Attend your thesis defense and ask questions.
  • Evaluate your thesis (written and oral) and decide if you pass, providing additional feedback and requesting any changes to the written document.

Step 1d: Proposal Review

If you are graduating in December, then by 11:59 pm on August 10th, you need to send your thesis proposal (described in step 1b) to your committee members (described in step 1c). This should be sent as a single email which is sent to your research advisor and the other two committee members, with your academic advisor(s) CC'd.

If you are graduating in May, then by 11:59 pm on January 10th, you need to send your thesis proposal (described in step 1b) to your committee members (described in step 1c). This should be sent as a single email which is sent to your research advisor and the other two committee members, with your academic advisor(s) CC'd.

Within 2 weeks, the committee members need to acknowledge the proposal and submit comments to the student.  If the committee members request revisions, then a revised proposal is due to the committee and academic advisor 2 weeks later and is subject to final approval by the thesis committee and the program Steering Committee.

Step 2: Research & Progress Report

If you are graduating in December, the thesis progress report (described immediately below) must be emailed to your research advisor, your other committee members, and the  dbrasier@cmu.edu no later than 11:59 pm on October 15th. If you are graduating in May, the thesis progress report (described immediately below) must be emailed to your research advisor, your other committee members, and the  dbrasier@cmu.edu no later than 11:59 pm on March 15th. If you cannot submit it by then and you are taking thesis for credit, you will be required to switch out of the thesis course. Please also note that this means you may not be able to count your research toward graduation in the same way as you had planned. Exceptions are only possible in cases of medical emergencies or other unusual circumstances and will require documented review by the office of Student Affairs. Please note as well that significant medical issues may also prompt a leave of absence and delay graduation.

It is expected that the student will be conducting research and data analysis during the entire academic year leading up to thesis defense and graduation.  The student should be meeting regularly with their advisor and other lab personnel and/or collaborators.  The thesis committee and academic advisor should be consulted by the student and/or advisor when challenges arise.  A formal progress report is due to the committee and academic advisor 2 months prior to graduation.  This progress report should follow include a summary of results and progress on each specific aims and any changes to experimental design or research plan. Completion of this progress report is required for all students enrolled in 03-700.

Step 3: Plan and Write Thesis

If you are graduating in December, a final written thesis needs to be emailed to your research advisor, thesis committee, and  dbrasier@cmu.edu no later than November 15th at 11:59 pm. If you are graduating in May, a final written thesis needs to be emailed to your research advisor, thesis committee, and  dbrasier@cmu.edu no later than April 15th at 11:59 pm. If you cannot submit it by then and you are taking thesis for credit, you will be required to switch out of the thesis course. Please also note that this means you may not be able to count your research toward graduation in the same way as you had planned. Exceptions are only possible in cases of medical emergencies or other unusual circumstances and will require documented review by the office of Student Affairs. Please note as well that significant medical issues may also prompt a leave of absence and delay graduation.

Writing the thesis typically takes 3 months.  A template is available here. The thesis should have the following sections:

  • Title page & Dedication/Acknowledgements
  • Abstract (1 page)
  • Introduction chapter (4 or more pages). Separate from introduction sections in other chapters, this is a place for the student to put the entire thesis in context.
  • 1 or more additional chapter (20 or more pages each). Chapter format should be consistent and may match the format of any journal article in the field of study.
  • Bibliography (pages are enumerated but do not count toward page total). This may be a standalone bibliography for the whole thesis or each chapter may have its own bibliography.

Step 4: Thesis defense

Please review the academic calendar. Your thesis defense needs to be at least 2 weeks before the last day of final exams in the semester you are graduating. Planning and scheduling should begin well in advance. Please also note the steps below.

Step 4a: Schedule & Plan the Thesis Defense

If you are graduating in December, you need to email your research advisor, your committee members, and CC dbrasier@cmu.edu no later than 11:59 pm on October 15th to begin the process of planning the defense date and time. If you are graduating in December, you need to email your research advisor, your committee members, and CC dbrasier@cmu.edu no later than 11:59 pm on March 15th to begin the process of planning the defense date and time. If you cannot send this email by then and you are taking thesis for credit, you will be required to switch out of the thesis course. Please also note that this means you may not be able to count your research toward graduation in the same way as you had planned. Exceptions are only possible in cases of medical emergencies or other unusual circumstances and will require documented review by the office of Student Affairs. Please note as well that significant medical issues may also prompt a leave of absence and delay graduation.

Please communicate actively with your committee. A final date and time needs to be agreed upon by the whole committee no later than the same time as the due date for the written thesis (see step 3, above). Each member of the committee needs to send confirmation to the student that they will be able to attend the agreed upon thesis date. The student must collect and save these emails by the due date for the written thesis (see step 3, above). Exceptions are only possible in cases of medical emergencies or other unusual circumstances and will require documented review by the office of Student Affairs. Please note as well that significant medical issues may also prompt a leave of absence and delay graduation.

If the student does not receive written email confirmation from each committee member that they can attend the thesis defense on the agreed date and time by the due date for the written thesis (see step 3, above), then the student must email their academic advisor immediately. Delays in confirming a date and time for the thesis will result in receiving a failing grade in the thesis course or (in cases where the student can demonstrate that there are extenuating circumstances) an incomplete grade. Note as well that incomplete grades will delay your graduation even in cases where you are not at fault. Please plan early.

Note as well that the latest possible date for the defense is the 1st day of the month you are graduating. Later than that will result in you either receiving a failing grade in your thesis or receiving an incomplete grade. Note that incomplete grades will delay your official graduation date to a later semester.

Once a date is determined and a location has been reserved (with help from your thesis advisor), send an email to the committee members and your academic advisor notifying them of the date, time, and location of your defense. This should be done no later than November 1st (for December graduates) or April 1st (for May graduates).

All members of the thesis committee must be present for the defense (in case of an emergency on the day of the thesis necessitating remote attendance, a committee member may attend remotely). The defense will last between 1-2 hours. Once a date and time are selected the student should work with their thesis advisor to reserve a suitable room that can seat at least 10 people (or more if the student expects more). If the research advisor is unable to find such a room, the student needs to email the academic advisor immediately.

Step 4b: Publicize the Defense Date

Two weeks before the defense, the student should email the following to the Academic Advisor:

  • Thesis title
  • Research Advisor and committee members’ names and department (also university affiliation for any committee member whose primary affiliation is not Carnegie Mellon)
  • Location, date and time of defense
  • A photograph of yourself *or* an image from your research (could be panel from a figure or a nice sketch related to your work)
  • A one paragraph abstract for your thesis

The department(s) will be invited. The student should also invite others to attend the event.

Step 4c: Finish Thesis and Prepare Defense 

At least 2 weeks prior to the thesis defense, the student needs to submit a completed thesis document to the thesis committee and the academic advisor. This is why the written thesis (step 3, above) is due as described above. However, if you are defending your thesis early, then note that your written thesis needs to be completed similarly early. If you are unable to submit a completed thesis to your committee by the deadline of 2 weeks before the defense date, then you are required to email all of your committee members and CC dbrasier@cmu.edu to request a later date. The request needs to specify when you actually will have the completed thesis ready to send to the committee. Note that even in cases of documented emergencies, extensions of this deadline are unlikely to be granted. If all members of the committee agree to a later submission, then it will be allowed provided that such a delay is short enough that it will not disrupt the ability of the committee to review the document prior to the defense date. Note as well that a second request for an even later submission is not possible except in situations where the student experiences a severe enough disruption to their academic work that they need to take a formal leave of absence from the university.

It is recommended that the student practice the thesis defense presentation with the lab members and/or advisor.

Step 4d: Thesis Defense

As mentioned in step 4a, the latest possible date for thesis defense is 2 weeks before the last day of the final exams in the semester that the student is graduating. On the agreed date and time, the student will present their thesis in the agreed location.

After a public defense and public questions, the student will remain for private questions with the committee and then the committee will confer privately without the student.

The committee will come to a consensus about the student's outcome for the thesis. In cases where unanimity is not reached, a vote is taken with the outcome that receives a majority vote being the result. The possible outcomes for the thesis are as follows:

  • Unconditional pass. This means that the candidate passes the defense immediately. There may be small revisions requested for the written document, but the committee members do not believe that any of the changes are necessary for the student to pass the thesis.
  • Conditional pass. This means that the candidate has done sufficient work to warrant a pass; however some issues remain with the scientific rigor or interpretations of the thesis. The committee will present the candidate with a written list of requested revisions to the thesis document, clearly denoting which changes are essential for the candidate to pass the thesis and which (if any) are minor changes that are not strictly necessary to secure a passing grade. The candidate then has until the last day of the final exam period to make the changes and submit the revised thesis to the committee for re-evaluation to receive either a "pass" or "fail" grade.
  • Fail. This means that the science done is insufficient for a passing grade on the thesis.

Step 5: Revisions

Any revisions that the committee requests to the written thesis need to be completed and returned promptly to the committee. Specifically, a final version of the written thesis with all requested revisions must be emailed to the faculty advisor, the committee members, and dbrasier@cmu.edu no later than 11:59 pm on the last day of the final exam period of the semester of graduation.