Certificate in Biomedical Informatics

The IBI Certificate in Biomedical Informatics is a four-course sequence for non-informatics professionals designed to build the informatics community at Penn and to train informatics-literate clinicians and researchers who will have a broad understanding of the field of biomedical informatics.

This certificate is unique among Philadelphia-area programs in that its curriculum covers general biomedical informatics, clinical informatics, and clinical research informatics.

Students in the Certificate in Biomedical Informatics Program can expect to obtain a working knowledge of biomedical informatics, its history, the current landscape, and future directions of the field. The four courses in this program also form the core of the Master of Biomedical Informatics (MBMI) program, so certificate students can expect to interact with a variety of students with diverse interests in informatics.

Certificate students who wish to expand their biomedical informatics skills in a degree program may apply to the MBMI program and, if accepted, may transfer credit from the certificate program to meet the requirements of the Master’s program. Contact Hannah Chervitz for details about this process.

The certificate curriculum is designed to:

  • Provide exposure to the field to those working in biomedical practice or research who would like to be “informatics aware”
  • Build a community of those who can collaborate with informaticians and health information technology personnel
  • Provide those with an interest in informatics opportunities to learn more about the field

Additionally, each course include hands-on experience in an active learning environment to increase skills and reinforce knowledge, such as:

  • Informatics journal club to build critical appraisal skills
  • Programming exercises
  • Database development and manipulation assignments
  • Practice in proposal writing and oral presentation for informatics projects


Required courses:

Introduction to Biomedical and Health Informatics (BMIN 501). Fall semester; Thursdays, 4-7pm. Course director: John H. Holmes, 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.)

Databases in Biomedical Research (BMIN 502). Spring semester; Tuesdays, 4-7pm. Course director: John H. Holmes, 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.)

Data Science for Biomedical Informatics (BMIN 503). Fall semester; Tuesdays and Thursdays, 1:30-3pm. Course director: Blanca Himes, PhD. This course will use 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 exploratory analyses, build 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 R and github.  (This course has been offered in the past as EPID 600.)

Special Topics in Biomedical and Health Informatics (BMIN 504). Spring semester; Mondays 5-8pm. Course director: Jason Moore.

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


Additional program requirements

  • Collaborative Institutional Training Initiative online training in Responsible Conduct of Research
  • Human Subject Research Training
  • Participation in the annual Informatics Day Symposium

Certificate Program Director: John H. Holmes, PhD, FACE, FACMI

Administrative Director: Hannah Chervitz

Advisory Committee

  • Kathryn H. Bowles, PhD, RN, FAAN, FACMI
  • Graciela Gonzalez, PhD
  • Blanca E. Himes, PhD
  • Jason H. Moore, PhD, FACMI
  • Anthony Luberti, MD, MS

Courses will be charged a tuition rate of $4,286 per course unit and general fees of $348 per course unit.

Tuition and Fee Breakdown for 2018-2019 academic year:

Fall/Spring Tuition General Fee Total
1 C.U. $4,286 $348 $4,634
2 C.U. $8,572 $696 $9,268
  • Note: The certificate has a total of 4 course units

This program is not eligible for federal financial aid programs, but tuition benefits are available to qualifying faculty and staff.  Non-qualifying postdoctoral fellows, clinical fellows, and house staff are eligible for internal financial aid.  Contact the program directly for details, as the application process is slightly different.

At this time, only faculty, staff, research/clinical fellows, and students affiliated with the University of Pennsylvania, Penn Medicine, or Children’s Hospital of Philadelphia are eligible to apply.

The application deadline for Fall 2019 matriculation is March 31, 2019.

  1. All eligible applicants will apply online via CollegeNet:
    • Once you have created a CollegeNet account, you can then begin your online application. After logging in, select “Online Application”.
    • You will be asked to enter your personal information.  Save and continue to program information.
    • The Certificate program applications are found under “Perelman School of Medicine Masters Programs”.
    • Applicants should select: “Biomedical Informatics, Certificate Program”
    • Applicants may access their application any number of times until submission. Once the application has been fully submitted, applicants can check the status by logging into the system.
  2. Applicants are required to submit :
    • Curriculum Vitae
    • Personal statement: a one page description of career goals that includes a description of how the certificate meets your educational objectives
    • Transcripts
      • Upload an unofficial transcript to the online application form
      • If you are admitted to the program, official transcripts must be delivered directly to Penn from your institution, via email or mailed to Hannah Chervitz at D204 Richards Building, 3700 Hamilton Walk, Philadelphia, PA 19104.
    • There is a $75 application fee.

What is Biomedical Informatics? Is it the same as bioinformatics?


According to the American Medical Informatics Association:

Biomedical informatics (BMI) is the interdisciplinary field that studies and pursues the effective uses of biomedical data, information, and knowledge for scientific inquiry, problem solving and decision making, motivated by efforts to improve human health.


  • BMI develops, studies and applies theories, methods and processes for the generation, storage, retrieval, use, and sharing of biomedical data, information, and knowledge.
  • BMI builds on computing, communication, and information sciences and technologies and their application in biomedicine.
  • BMI investigates and supports reasoning, modeling, simulation, experimentation and translation across the spectrum from molecules to populations, dealing with a variety of biological systems, bridging basic and clinical research and practice, and the healthcare enterprise.
  • BMI, recognizing that people are the ultimate users of biomedical information, draws upon the social and behavioral sciences to inform the design and evaluation of technical solutions and the evolution of complex economic, ethical, social, educational, and organizational systems.

In contrast, bioinformatics is concerned with the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data.

Does this program provide training in bioinformatics tools and techniques?

Although many of the principles taught in our certificate courses are applicable to bioinformatics, only Data Science for Biomedical Informatics includes practical bioinformatics training as part of its syllabus.  Students who are looking for coursework in bioinformatics, rather than biomedical informatics, may want to consider other programs.

Are there any prerequisites?

None of the courses in the certificate program have any specific prerequisite coursework, but students should have a Bachelor’s degree or higher, and at least one year of clinical or biomedical research experience.

What is the timeline for this program?

Most students will complete the program in 1-2 years. Because biomedical informatics is a rapidly changing field, students must meet all requirements within 3 years of their matriculation in order to receive the certificate.

What sort of financial aid is available?

This program is not eligible for Title IV financial aid. Penn faculty and staff may use tuition benefits toward this program.