Perelman School of Medicine at the University of Pennsylvania

Master of Biomedical Informatics


Course Descriptions

The following courses are required for all MBMI students (click the arrow for details about each course):

BMIN 5010: Introduction to Biomedical Informatics

Offered during the fall semester, Mondays, 3:30-6:30pm (1 CU) On-Line


Course director: Fuchiang (Rich) Tsui, PhD

This course is designed to provide a survey of the major topics areas in medical informatics, especially as they apply to clinical research.  Through a series of lectures and demonstrations, students will learn about topics such as databases, natural language, clinical information systems, networks, artificial intelligence and machine learning applications, decision support, imaging and graphics, and the use of computers in education. (This course has been offered in the past as EPID 632.)

* Prerequisites: 

  • (RECOMMENDED)  Basic familiarity with Biomedical Concepts.
  • (REQUIRED) Knowledge of basic Pathophysiology.


BMIN 5020: Database and Data Integration in Biomedical Research

Offered during the spring semester, Tuesdays, 1:45-4:45pm (1 CU)

Course director: Dokyoon Kim, PhD

This course is offered during the spring semester and is intended to provide in-depth, practical exposure to the design, implementation, and use of databases in biomedical research. This course is intended to provide students with the skills needed to design and conduct a research project using primary and secondary data. Topics to be covered include: database architectures, data modeling approaches, data normalization, database implementation, client-server databases, concurrency, validation, Structured-Query Language (SQL) programming, reporting, maintenance, and security. All examples will use problems or data from biomedical domains. MySQL will be used as the database platform for the course, although the principles apply generally to biomedical research and other relational databases.  (This course has been offered in the past as EPID 635.)


  • (REQUIRED) Knowledge of basic Pathophysiology.


BMIN 5030: Data Science

Offered during the fall semester, Tuesdays and Thursdays, 1:45pm-3:15pm (1 CU) 

Course director: Blanca Himes, PhD 

In this course, we will use RStudio/R and other freely available software to learn fundamental data science applied to a range of biomedical informatics topics, including those making use of health and genomic data. After completing this course, students will be able to retrieve and clean data, perform explanatory analyses, build and evaluate models to answer scientific questions, and present visually appealing results to accompany data analyses; be familiar with various biomedical data types and resources related to them; and know how to create reproducible and easily shareable results with RStudio/R and GitHub.

Recommended prerequisite: Introductory-level statistics course. Familiarity with programming or a willingness to devote time to learn it. NOTE: Non-majors need permission from the department.



BMIN 5040: Special Topics in Biomedical and Health Informatics

Offered during the spring semester, Wednesdays, 3:30-6:30pm (1 CU)


Course director: Marylyn D. Ritchie, PhD

This course is designed to provide an in-depth look at four topics that are of essential importance in biomedical informatics. Each topic will be allotted four consecutive weeks in the class schedule, as four modules, with the intention that each module becomes its own “mini-course”. The topics for each module may rotate from semester to semester, based on these criteria:

  • Historical importance to the current field of biomedical informatics research and/or practice
  • Cutting-edge developments in biomedical informatics
  • Topics not covered in depth in BMIN 501
  • Consensus of the program leadership and teaching faculty

Possible modules include:

  • Deep learning methods for mining biomedical data
  • Visualization analytics for clinical research
  • Methods for integration of observational and ecological data for public health surveillance
  • Informatics implications for distributed research networks
  • Human computer interaction and patient safety
  • Nature-inspired analytics for biomedical informatics
  • Network science applications in biomedical informatics
  • Intersections of clinical research, clinical and clinical research informatics, and clinical decision making

* Prerequisites:

  • (REQUIRED) BMIN 501: Introduction to Biomedical and Health Informatics
  • (REQUIRED) Knowledge of basic Pathophysiology.
  • (RECOMMENDED) BMIN 502 Databases in Biomedical Research and BMIN 503 Data Science


BMIN 5060: Standards and Clinical Terminologies

Offered during the first half of the fall semester, Wednesdays, 4:00-6:30pm (.5 CU)

Course director: Michael Padula, MD, MBI

This survey course is designed to provide an overview of health information standards and clinical terminologies.  Through a series of lectures, demonstrations, and hands-on exercises, students will learn about topics such as standards, interoperability, data modeling, vocabularies, and health information exchange. 

* Prerequisites:

  • (RECOMMENDED) BMIN 501: Introduction to Biomedical and Health Informatics
  • (REQUIRED) Knowledge of basic Pathophysiology.


BMIN 5070: Human Factors

Offered during the second half of the fall semester, Wednesdays, 4:00-6:30pm (.5 CU) On-Line

Course directors: Ross Koppel, PhD and Julia Szymczak, PhD

The course will cover five main topic areas: 1. usability, 2. evaluation and measurement of usability, 3. workflow, 4. user-centered design, 5. implementation, and 6. continuing improvement/optimization. Each topic area will incorporate principles, methods, and applications. In the principles section for each topic, the course will clearly define terminology related to the topic area (e.g., What is workflow?), review how key concepts relate to each other (e.g., relationship between human factors engineering and human-computer interaction), and examine the relevance of the topic area in Applied Clinical Informatics. The methodology section for each topic will address qualitative, quantitative, and computational methods used for the design, implementation, and evaluation of health information technology. The applications section for each topic will use case studies based in the topic area to examine the real-world application of principles and methods. The course will cover a wide range of contexts, from homes/communities to organizations to a broader regional scale.

* Prerequisites:

  • (RECOMMENDED) BMIN 506: Standards and Clinical Terminologies 
  • (REQUIRED) Knowledge of basic Pathophysiology.


BMIN5080: Biomedical Information Systems Analysis and Design

Offered during the spring semester, Mondays, 3:30-6:30pm (1 CU)

Course Directors: John Holmes, PhD

This course provides an introduction to the concepts and principles of information systems analysis and design, focusing on the techniques of the Unified Modeling Language and the Unified Process, specifically as these apply to healthcare settings. As a result, there is a strong emphasis on applying these techniques to real-world issues with clinical and clinical research information systems. These include the electronic health record, information systems in clinical specialties, and systems to support the management of data used for clinical research and healthcare administration.

This course is required for MBMI students in the Healthcare Quality Informatics Track.


  • (REQUIRED) Knowledge of basic Pathophysiology.


HPR 6200: Implementation Science

Offered during the spring semester (1 CU)

Course Directors: Danielle Cullen, MD, MPH, MSHP and Emily Becker-Haimes, PhD

This course presents a survey of the field of implementation science in health. The structure of the course will include two parts. In the first part, we will introduce the field of implementation science, with an emphasis on theory, design, and measurement. In the second part, we will focus on applied implementation science which will include examples of research programs in implementation science as well as applying insights from implementation science to practical implementation. An emphasis on qualitative and mixed methods approaches is included.


  • (REQUIRED) Knowledge of basic Pathophysiology.


BMIN 9900: Capstone

Offered fall, spring and summer semesters (1 CU)

With mentorship from their Capstone Advisor, students will develop and present the results of a clinical informatics project relevant to their interests. During this semester-long course, students will attend a weekly seminar in which they develop, propose, implement, and present their capstone project. Students meet with regularly with their Capstone Advisor, who is also invited to attend the seminars. The seminar affords both students and advisors the opportunity for cross-fertilization of ideas and skills, and ultimately the honing of projects to a high level of value for the students and the clinical environments in which they conduct their projects.


  • (REQUIRED) Minimum of 7 CUs of the required coursework of the MBMI Program
  • (REQUIRED) Knowledge of basic Pathophysiology.


In addition, students must take 2 course units (CUs) of elective coursework. Possible electives include, but are not limited to:

          Consumer and Personal Health Informatics (BMIN 5090)

          Clinical Research Informatics in the Cloud:  Analytic Workflows and Infrastructure (BMIN 5100)

          Foundations of Artificial Intelligence in Health (BMIN 5200)

          Advanced Methods and Health Applications in Machine Learning (BMIN 5210)

          Natural Language Processing for Health (BMIN 5220) 

          Introduction to Python Programming (BMIN 5250)

          Introduction to Machine Learning (CIS 5190)

          Big Data Analytics (CIS 5450)

          Data Visualization and Interaction Design (CIS 5600)

          Organizational Project Management (DYNM 6190)

          Process Improvement Tools and Strategies (DYNM 6340)

          Longitudinal and Clustered Data (EPID 6210)

          Data Mining (ESE 5450)

          Introduction to Bioinformatics (GCB 5350)

          The American Health Care System (HCIN 6000)

          Health Care Operations (HCIN 6010)

          Behavioral Economics and Decision Making (HCIN 6020)

          Health Care Innovation (HCIN 6022)

          Evaluating Health Policy and Programs (HCIN 6030)

          Health Economics (HCIN 6040)

          Translating Ideas Into Outcomes (HCIN 6070)

          Leading Change in Health Care (HCIN 6170)

          Medical Devices (HCMG 8530)

          Comparative Health Care Systems (HCMG 8590)

          E-Health: Business Models and Impact (HCMG 8660)

          Qualitative Methods Research (HPR 5030)

          Principles and Practice of Quality Improvement and Patient Safety (HPR 5040)

          Clinical Economics and Decision Making (HPR 5500)

          Systems Thinking in Patient Safety (HPR 6500)

            Applied Predictive Modeling for Health Services Research (HPR 6600)

          Decision Models and Uncertainty (OIDD 6210)

          Decision Support Systems (OPIM 6720)

          Health Communication in the Digital Age (PUBH 5650)

Courses not on the above list must receive approval from the Program Director. Transfer of credit from external institutions may be possible for some students, subject to approval.