MSAS Research Thesis Requirements and Timeline

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.

Step 1: Thesis Proposal

We recommend that you begin thesis proposal preparation 9 months prior to graduation, but it must be completed at least five months before graduation.

Step 1a: Pre-Proposal Planning

Students meet with their planned thesis advisor at least 5 months prior to graduation (preferably 9-12 month 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 jkangas@andrew.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, which is done 02-700.

Step 1b: Proposal Writing

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, approx. 0.5 page). State concisely and realistically what your research is intended to accomplish and what hypotheses are to be tested.
Background & Significance (approx. 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

The student and advisor should identify at least two other faculty committee members. 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 Computational Biology Department; if the thesis advisor is not a tenure-track professor, 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.

Step 1d: Proposal Review

At least 5 months prior to the student’s planned graduation date, the completed proposal (which must have already been reviewed by the thesis advisor, see step 1b, above) should be e-mailed to jkangas@andrew.cmu.edu (academic advisor), plus the full thesis committee, with the advisor CC’ed. Within 2 weeks, the committee members need to acknowledge the proposal and submit comments to the student. 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 directors.

Step 2: Research & Progress Report

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 3 months prior to graduation. This progress report should include a summary of results and progress on each specific aim and any changes to experimental design or research plan.

Step 3: Plan and Write Thesis

Writing the thesis typically takes 3-5 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: Schedule & Plan the Thesis Defense

The thesis defense must be completed at least 2 weeks prior to graduation. Planning and scheduling should begin well in advance. All members of the thesis committee must be present for the defense. The defense will last between 1-2 hours. Once a date and time are selected the student should work with either the academic advisor or the thesis advisor to reserve a suitable room that can seat at least 10 people (or more if the student expects more).

Step 5: Publicize the Defense Date

Student contacts the Program Coordinator and Academic Advisor with:

Defense title
Research Advisor and committee members’ names (external committee member's school and dept. must be listed)
Date and time of defense
Location (Reserved room)

A research-related photograph should also be provided. The program coordinator will design a flyer and post it throughout the Gates-Hillman Complex and will also send an email to the department to publicize the event. The student may also invite others to attend the event.

Step 6: 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. It is strongly recommended that the student practice the thesis defense presentation with the lab members and/or their advisor.

Step 7: Thesis Defense

The student should bring a copy of the MS Thesis Defense Form with name, laboratory, & thesis title filled out to the defense. 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.

Step 8: Revisions

1-2 weeks following the defense, any requested revisions need to be submitted to the thesis committee and the academic advisor. After a 3 year embargo, completed thesis documents will be publicly available in ProQuest and/or program website.