Master's Thesis


BME 291 - MS Thesis/Project Preparation Seminar Syllabus [docx]
BME 298 - MS Project Syllabus [docx]
BME 299 - MS Thesis Syllabus [docx]

Required Report Writing Guidelines

BME Thesis/Project Report Style Guide [pdf]


Differences between MS Thesis and MS Project

There are few key differences between the Thesis and Project option. If you choose to do a Thesis, you will have to complete 6 units for that (BME 291, BME 298 and BME 299), compared to the 3 units required for the Project (BME 291, BME 298). Since the three courses (BME 291, BME 298 and BME 299) must be taken in a sequence, a Thesis usually requires at least three semester to complete, compared to the two or more semesters required for a Project.

The Thesis can only be pursued individually, so you won’t be able to share the workload with a team mate, unlike the Project.

Finally, the Thesis’ final deliverable is a dissertation, which needs to be approved by the College of Graduate Studies and published by Montezuma Publishing, a non-profit organization is SJSU's partner for review and publication of theses and dissertations. The review and approval process is based on high quality standards, and the time required for that usually takes the bulk of the BME 299 semester.

Reasons to choose the Thesis option over the Project include: (1) the student wants to pursue a PhD degree, and the Thesis provides the opportunity to prepare for higher-quality research work and earn one or more publications to support their application to PhD programs; (2) the student wants to improve their chance to land an R&D job in the private sector, and the experience and publications resulting from a Thesis can help with that; (3) personal accomplishment. 


Before you start your MS Thesis

Students should gear up for their MS Thesis at least one semester before they enroll in BME 291. In addition to clearing all the prerequisites for BME 291 (see MS-BME Degree Checklist [pdf]), the student should:

  • Identify topic areas of interest and one or more prospective technical advisors (usually, BME faculty)
  • Inquire with prospective technical advisors for available projects in the areas they identified
  • Reach out to potential Reading Committee members (for MS Thesis, you need at least two members in addition to your technical advisor)
  • Explore funding opportunities to support their project expenses
  • Consider whether they want to pursue a Project or Thesis

Once the Thesis topic and advisor have been identified, the student should start working on getting familiar with the topic. In particular, it is recommended that, before the beginning of their BME 291 semester, the student:

  • Select and critically review some peer-reviewed papers from the relevant literature
  • Draft a list of (tentative) specific aims for their MS Thesis

The Thesis Proposal

The Thesis is generally articulated into three components: proposal (BME 291), execution (BME 298/299) and dissertation writeup and revisions (BME 299). In the proposal, the student identifies the overall objective and articulate specific aims that will allow them to address the technological or clinical gap they identified with their literature review. In addition to demonstrate the significance and innovation of the proposed work, the student needs to show that their thesis is feasible by discussing in detail the materials and methodologies they will use.

Here is the general template for the structure of a MS-BME Thesis proposal:

  • Introduction
  • Literature review
  • Objectives / Specific aims
  • Materials and Methods

By the end of the semester (BME 291), the student must defend their proposal with an oral presentation, followed by a Q&A session with the course instructor, technical advisor and Reading Committee member(s).

The Thesis 

Once the student has successfully defended their proposal and cleared BME 291, they are eligible to enroll in BME 298. During this semester, the student will execute the proposed work, which may include device or protocol design and validation, benchtop experiments, numerical simulation. The data collected from those activities will have to be appropriately processed, analyzed, interpreted, evaluated in light of the information available from literature review and established clinical practice.

The writeup of the Thesis usually takes most of the BME 299 semester. For detailed instructions about Thesis preparation, review, approval and publication, the student should review the following materials:

Completion of the Thesis may require one or more semesters, depending primarily on the time committed by the student and the number of draft resubmissions requested by the College of Graduate Studies before the dissertation is approved. Delays external to the student’s control (e.g. purchase of backordered items, equipment needing repair or maintenance, and the intrinsic uncertainties of research work) may further add to the time required to complete the Thesis. If the work extends beyond the BME 299 semester, the student may be required to register for BME 1290R to maintain continuous enrollment.

By the end of the BME 299 semester, the student must defend their results and conclusions with an oral presentation, followed by a Q&A session with the course instructor, technical advisor and Reading Committee members.

Thesis close-out and handover

After the final Thesis has been formally approved by the Reading Committee and the College of Graduate Studies, the student should work with the BME 299 course instructor, technical advisor and Graduate Advisor to finalize the following items:

  • Submit a digital copy of your approved dissertation to the Graduate Advisor, along with a copy of the thesis information form (a.k.a. dissertation packet), with signatures of every reading committee member (and yours)
  • Forward to the Graduate Advisor a formal communication (usually an email) with the CGS approval of your dissertation
  • Obtain a CR grade in BME 298 and BME 299
  • Confirm with the Graduate Advisor that all the coursework listed in the approved candidacy form has been completed satisfactorily. Any deviation from the courses listed in the approved candidacy form requires the submission of a Course Substitution Request.
  • Hand over all the materials produced for the Thesis to the technical advisor, including:

          - all the peer-reviewed papers referenced in the report
          - all the deliverables generated (reports, slides, protocols,                     manuscripts, conference abstracts)
          - all the experimental/numerical data generated and analyzed
          - documentation and instructions for new equipment and software (not already documented), for the benefit of future students

  • Clear the lab space, refrigerator space, and return all the equipment borrowed for the Thesis.

After all the items above have been completed, the Graduate Advisor will submit a Verification of Culminating Experience form to GAPE, on behalf of the student. GAPE will award the MS degree shortly thereafter.