Master's In-person

Master of Science in Biomedical Informatics

Capstone Project Guidance

Introduction to the Capstone Project

The capstone project is a degree requirement of the Master of Science in Biomedical Informatics Program. Students complete their capstone projects during the last three quarters of their program. Students will use the skills and experience gained during the program to complete a biomedical informatics project with a sponsoring organization. The projects are conducted in groups of two students with mentorship from the student’s Scientific Advisory Committee (SAC), consisting of scientific advisors and capstone sponsor as well as the capstone course instructors.

Students enroll in three capstone classes scheduled in three consecutive quarters. Capstone projects start in either the Winter or Summer quarters.

Course Title Units Grading Term
MSBI 39901 Capstone Project
100 Graded Winter or Summer
MSBI 39902 Capstone Project
100 Graded Spring or Autumn
MSBI 39903 Capstone Project
Writing and Presentation
100 Graded Summer or Winter

In the first of the three courses, Capstone Project Proposal, students will develop their project. They document the scope of the project, and turn a problem statement, whether provided by a sponsor or developed independently, into an actionable plan for research. In the second course, Capstone Project Implementation, students will complete the bulk of their research. Even though research may or will have already gotten underway during the first quarter, students will be completing the bulk of their quantitative and qualitative research, data analysis, and other data collection methodologies during the second, Implementation quarter. In the third and final quarter, Capstone Project Writing & Presentation, students may complete their data collection and will write their final capstone paper, finalize any additional deliverables for the sponsor, and develop a presentation that summarizes their work.  They will present their work at the Capstone Showcase scheduled at the end of the third quarter.  All courses will have assignments and students will be assessed quality grades.

All students must meet standards for satisfactory academic progress as outlined in the Graham Student Manual to begin their capstone project. Students must not be on probation, must not have incomplete courses, and must possess at least a 3.00 cumulative GPA. Because the capstone sequence involves university-industry partnerships, a high degree of professionalism is expected of students during all phases of the capstone project.

Scientific Advisory Committee (SAC) Mentorship

The SAC provides mentorship and guidance to student teams throughout the capstone process. The SAC comprises 1-2 MScBMI instructors1, who serve as scientific advisors, and at least one representative from the capstone sponsor organization. Even though the scientific advisor and capstone sponsor are both on the SAC and may share certain competencies, they have distinct roles in the guidance and oversight they provide students.

Scientific Advisors

Program staff match MScBMI instructors as scientific advisors to capstone projects based on their subject matter expertise in an area of biomedical informatics. Scientific advisors should be regularly updated on progress of the project throughout the capstone process because they will grade the final capstone paper and presentation. In addition, they can advise students on appropriate sources, methodologies, and perspectives for their projects so that they can produce professionally relevant and rigorous research. 

Primary advisors should be available for every meeting to provide guidance and feedback. Secondary advisors will attend meetings if their schedules allow.  Both advisors should be included in meeting invites, progress update emails, etc.  Both advisors will be grading the final paper and presentation at the end of the Capstone Writing and Presentation quarter.

Meetings with scientific advisors should be held each quarter as follows:

  • Proposal Course: meet at least three times or approximately once per month to share finalized project scope and solicit feedback and subject matter advice.
  • Implementation Course: meet at least three times or approximately once per month to discuss data collection methodologies and preliminary analyses to ensure that high quality research is being conducted.
  • Writing & Presentation Course: meet at least three times or approximately once per month to discuss the final analyses, conclusions and recommendations derived from the research to ensure that the final capstone paper and presentation are thorough and rigorous.

Capstone Sponsor

The capstone sponsor provides direct oversight and supervision of the student team by guiding the goals and scope of the project. Typically, sponsors are seeking solutions to specific problems or aim to gain an understanding of issues of particular importance and relevance to their work. To ensure that student teams are working according to the expectations of the sponsor, student teams should connect with the capstone sponsor throughout the year. The meetings should occur as follows:

  • Proposal Course: two to three times to discuss and set project goals, scope, and deliverables.
  • Implementation Course: weekly or bi-weekly to report on findings and progress in data collection and to adjust the goals and scope of the project if necessary.
  • Writing & Presentation Course: two to three times to discuss findings and conclusions; and to confirm the structure of the final deliverable for the sponsor2.

Capstone Instructors

The capstone instructors and instructional assistants will also work closely with students. The instructional team will help match students to projects, provide guidance on the research process (generally) including research methods, the structure of the written work, the logic of the analyses and writing. The instructors are there to address questions about the process, set expectations for the level of work that is required, explain the principles of research, help student teams work together and organize their work, provide advice on how to address the concerns of the SAC and teach principles of writing. Capstone instructors may also meet with students between quarters. Students will meet with capstone instructors as follows:

  • Proposal Course: during weekly course meetings and by student team, at least once a month. Student teams are invited to meet with the capstone instructors whenever they have questions.
  • Implementation Course: during weekly course meetings or lab sessions, and by student team, at least once a month. Student teams are invited to meet with the capstone instructors whenever they have questions.
  • Writing & Presentation Course: during weekly course meetings and by student team, whenever necessary. Student teams are invited to meet with the capstone instructors whenever they have questions.

Finding a Project

MScBMI staff curate a catalog of projects for student teams and match students to these projects based on their preferences, skills, and professional experience. Even though matching to a project from the catalog is preferred, students may suggest a project idea. Please see below for details on matching to a project and requirements for proposing a project.

MScBMI project catalog

The MScBMI program has academic, industry, and non-profit partners that sponsor projects. Descriptions of these projects will be shared prior to the start of the Capstone Proposal Course. The capstone administrator, program staff and MSBI 39901 instructional team will facilitate the matching process between organizations and students and initiate introductory communication between the student teams and sponsors. The final decision on whether the student will be matched to the project will rest with the sponsor organization.

Student proposed project

If a student has a relevant project from an employer or professional network that could be submitted as a capstone project, it must be approved by the MScBMI program staff, capstone administrator and instructional team. The proposed project is required to be different from day-to-day work duties and must have a detailed scope and goals that address the needs of the sponsor and the field of biomedical informatics. The student (or student team) must identify a capstone sponsor who would provide adequate supervision and must work with the sponsor to decide on a final deliverable for the sponsor. If a student is interested in moving forward with an independently proposed project, the project problem statement and description must be submitted in advance of the start of the Capstone Proposal quarter by the deadline communicated by the capstone administrator. 

Capstone Courses

During the first quarter of the project students will develop a capstone project proposal. In this graded course, students will complete different sections of the proposal as assignments and will revise their work to produce a strong draft by the end of the quarter. In addition, students will be required to meet with scientific advisors and sponsors on a regular basis. (See below.) All assignments are set by the MSBI 39901 instructor and are included in the syllabus on the Canvas course site. Note: Peers may be asked to provide feedback on the work of their partner. Sponsors may also be asked to provide feedback on the work of the student teams.

Sections of the Proposal

The project proposal may include any or all of the following sections. (These should be reviewed with your SAC before collecting data in the Implementation phase.)

  • The problem statement should include a brief description of the specific biomedical informatics problem or research question.
  • Research questions should indicate the goals of the research.
  • Introduction, Background and Significance should provide context for the problem that will be addressed. This could include descriptions of the organizations that may be part of the focus of the research, history of laws that are pertinent to the problem, discussions of biomedical informatics concepts and considerations that are relevant to the problem, and the like. The precise content of the background section will depend on the problem being addressed in the research. Again, the background section establishes the context and the relevant information that would make the problem intelligible.
  • The Literature Review includes a review of the relevant literature pertaining to the proposed problem/project. The purpose is to establish what is already known about the focus of research and to determine if there are gaps in the research. The literature review also presents controversies and debates. The literature review can provide the rationale for the research that the MScBMI student team is undertaking. The precise content will depend on the project.
  • The methodology section lays out the anticipated methods that will be used for data collection. It will also include the type of analyses that will be conducted and what type of data will be needed. Methods that have been previously used include, but are not limited to, surveying and interviewing professionals in the field, conducting a case study, reviewing media reports, and analyzing quantitative data.
  • A timeline of dates by which each step and milestone will be accomplished should be included, along with a description of any potential obstacles.

Note: Proposals should present a well-defined project, but projects continue to evolve. A proposal cannot anticipate all the insights and challenges that would cause the project to change. However, the proposal still helps to guide the project. As the project progresses, sections of the proposal may be revised, and changes reflected in the final paper.

IRB Review

A project that involves human subjects must be reviewed by the University of Chicago Institutional Review Board (IRB). According to the UChicago Social and Behavioral (SBS) IRB office, human subjects research includes but is not limited to:

  • Studies that collect new data through intervention or interaction with individuals (e.g., interviews, surveys) and yield information about the individuals including their opinions, views, and thoughts on various topics (e.g., surveys about alcohol consumption, interviews on experience with active shooter situations),  
  • Studies that produce generalizable knowledge about categories or classes of subjects from individually identifiable information, or
  • Studies that use human beings to evaluate environmental alterations, for example, weatherization options or habitat modifications to their living or working space or test chamber.

Projects which are not currently covered under existing IRB protocol and involve human subjects must be submitted for IRB review. Students must submit project details to the capstone instructors by the deadline established and no later than the start of month 2 of the Capstone Proposal course, see supporting document “MScBMI IRB Review.” The instructional team will aggregate project information and submit to the director of the SBS IRB who will determine whether each project must submit an application online via AURA.

During the second quarter of the capstone process the student team will execute the research plan outlined in the capstone proposal. Student teams are expected to spend at least 100 hours on the project throughout each quarter (equivalent to the time spent on a typical 100-unit course), but research can be unpredictable, and more time may be required. To ensure that students stay on track with their data collection and analyses, the MSBI 39902 instructor will require assignments requesting students share preliminary data collection results and project status. These assignments will be included in the syllabus and on the Canvas course site. Note: Peers may be asked to provide feedback on the work of their partner. Sponsors may also be asked to provide feedback on the work of the student teams.

During the Capstone Implementation course, students are expected to adhere to the following: 

Regular Communication with the Sponsor

The project proposal should include a timeline and description of communication with the sponsor, including how and when check-ins will occur. Students should be checking in with their sponsors on a regular basis, whether that means weekly or biweekly, and in-person or virtually. Students should report any obstacles to fulfilling this requirement to the capstone instructor and program staff.

Regular Communication with Scientific Advisors

The project proposal should include a timeline and description of communication with scientific advisors. Regular communication with the scientific advisor about progress, course corrections, and challenges will help manage uncertainty. Regular meetings with scientific advisors will also help address unexpected outcomes, will help avoid errors in the analysis, and will help strengthen the methods and results. Weekly, bi-weekly or at a minimum 3x quarter meetings are recommended depending on advisor availability. Students should report any obstacles to fulfilling this requirement to the capstone instructor and program staff.


All students must abide by the sponsor and University of Chicago standards for professional behavior, appearance, and communications during the capstone sequence. When students are working on their capstone project, they are representing themselves, their group, and the University of Chicago as biomedical informatics professionals. If the expectations are unclear regarding onsite business attire, the sponsor should be contacted before visiting the site. Because capstone projects involve crucial communications with the sponsor and/or with the MScBMI team, UChicago email should be used for all official interactions. Voicemail should also be checked regularly for sponsor communications.

Even though student teams may still be finalizing data collection and reporting results, the final course of the capstone process focuses on writing the final paper and developing a presentation. Students will be graded on assignments created by the MSBI 39903 instructor. Assignments mainly consist of drafts of various sections of the paper. Due dates are included in the syllabus and on the Canvas course site. Note: Peers may be asked to provide feedback on the work of their partner. Sponsors may also be asked to provide feedback on the work of the student teams.

Course requirements include:

Capstone Final Paper

At the end of the final quarter of the capstone process, student teams will submit a research paper as a capstone course and MScBMI degree requirement. The final paper may also be submitted to the capstone sponsor for their review.

All final papers will have the essential components of an academic paper as outlined by the instructor in the syllabus and Canvas course site (e.g., abstract, introduction & background, methods, results, discussion/conclusion, literature review, references, and appendices) and should be no more than 50 pages in length (not counting references and appendices). 

Even though every team must submit a final academic research paper as a degree and capstone requirement, the project sponsor may request additional, written deliverables different from the capstone paper. The scope and format of additional deliverable(s) should be predetermined with the sponsor during the Capstone Proposal course and discussed with the capstone instructional team. The following are examples of deliverables which may be requested by a sponsor: 

  • White Paper - A white paper advocates for a certain technical position or solution/tool (e.g., best practices or guidelines) to address a particular problem.
  • Data analysis, research summary and report on results – The specific format should be discussed with the sponsor.
  • Other – Defined by the sponsor organization.

Capstone Final Presentation

All capstone students are expected to develop a presentation of their work and provide a project summary at the MScBMI Capstone Showcase.  All team members are expected to speak during their presentation.

Presentation Format and Help

Students will develop the presentation using a PowerPoint template that is accessible on the Canvas capstone course sites. Students are expected to reach out to their SAC to solicit feedback, practice, and fine-tune the presentation. Students should be prepared to rehearse their presentations before the showcase.

Elements of the Presentation

Presentations must include key elements from the project proposal and final paper as noted below.  Requirements will also be outlined by the instructor in the syllabus and Canvas course site:

  • Statement of the problem.
  • Background and significance of the project.
    • Methodology, data, and resources used.
    • Results and findings.
  • Interpretations of results linking to problem statement.
    • Recommendations that emerged from the research.
    • Limitations and potential next steps.

Capstone Project Grading

The grade for MSBI 39903 Capstone Writing & Presentation will comprise the following elements:

Written document

The final academic research paper will account for a major percentage of the final grade. It is graded by the scientific advisor(s). The final paper may also be shared with the capstone sponsor in addition to any deliverables specifically requested by the sponsor.

Capstone Showcase Presentation and Q&A

Scientific advisors will score presentations of projects assigned to them during the capstone showcase and provide written feedback. All scores will be averaged and included in the final course grade.

Course assignments as outlined in syllabus by instructional team

Note: Rubrics used for grading the final paper and presentation and the weighting of each component will be outlined in the syllabus and/or on the Canvas course site.

MScBMI Capstone Project Timeline

Before Capstone Courses Begin

  • Attend or review a capstone information session.
  • Update resumes.

Pre-Quarter Capstone Proposal

  • Review capstone project catalog.
  • Complete the Capstone Preferences Survey.
  • Complete all pre-quarter assignments as outlined by MSBI 39901 instructor and capstone administrator.
  • Prepare for the IRB process by completing CITI training and applying for an AURA account.

Capstone Proposal

  • Finalize project and student match.
  • Student teams host introductory meeting with SAC – sponsor, advisors, and instructional team member(s).
  • Complete all assignments as outlined by MSBI 39901 instructor.
  • Regularly meet with the sponsor to finalize project scope, goals for the project and any additional deliverables for the sponsor.
  • Regularly meet with scientific advisors to receive feedback on the project proposal.
  • Submit project information to capstone instructors for determination of IRB application.
  • Submit final capstone project proposal.
  • Complete peer evaluations if required.

Capstone Implementation

  • Complete all assignments as outlined by MSBI 39902 instructor.
  • Execute project plan: conduct research, collect data and follow expectations defined in the capstone proposal.
  • Check in (weekly or bi-weekly) with sponsor contact.
  • Check in (weekly, bi-weekly or at a minimum 3x quarter) with scientific advisors.
  • Share assignments with scientific advisors.
  • Complete peer evaluations if required.

Writing and Presentation

  • Complete all assignments as outlined by MSBI 39903 instructor.
  • Check in with SAC while writing the final paper and presentation.
  • Complete peer evaluations.
  • Submit final capstone project paper.
  • Develop capstone project presentation.
  • Present at the MScBMI Capstone Showcase.
  • Share final paper with project sponsor.


  1. The program may also approve non-MScBMI faculty as a scientific advisor under special circumstances.
  2. It is possible that the sponsor will request a deliverable that is different from the capstone paper. If questions arise, please consult with the capstone instructional team.