Master's Degree

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New Fall 2019 Curriculum

To earn the Master’s degree in Biomedical Informatics, a trainee must complete a program of study approved by a committee of biomedical informatics faculty. This program must include successful completion of (a) the required coursework described below; (b) a research project involving significant research, design, or development work and a written report; and (c) a comprehensive examination composed by the Master’s committee.

All required courses must be taken for a letter grade, with the exception of the Journal Clubs, Biomedical Informatics Colloquiums and some Independent and/or Research Studies (to be determined by faculty advisors). A minimum grade of “B” is required in all graduate courses. The Master’s committee may waive course requirements that have been satisfied through prior university-level study, in accordance with the Committee on Graduate Studies guidelines. A trainee must comply with the regulations of the University of Pittsburgh (https://catalog.upp.pitt.edu/content.php?catoid=136&navoid=11853), as well as those regulations established by the biomedical informatics faculty. We expect that the average full time trainee will complete the degree in two years.

Up to 6 credits – grade “B” or better – from another institution or another department within the University of Pittsburgh can be considered for transfer towards the Biomedical Informatics Master’s degree. Acceptance of transfer credit must be discussed between the trainee and the advisor, and approved by Chair of Curriculum Committee.

The Master’s degree in Biomedical Informatics requires at least 36 credits that include 18 credits of required coursework, 1 credit of journal club, 3 credits of research, and 14 or more credits from additional courses, independent study, etc.

Foundations (15 required credits)

BIOINF 2070 Foundations of Biomedical Informatics 1 (3 credits)

BIOINF 2071 Foundations of Biomedical Informatics 2 (3 credits)

BIOINF 2118 Statistical Foundations of Biomedical Informatics (3 credits)

CS 1501 Algorithm Implementation (3 credits)

CS 2710 Foundations of Artificial Intelligence (3 credits)

Research Skills (4 required credits)

BIOINF 2032 Biomedical Informatics Journal Club (1 credit)

BIOINF 2134 Publication and Presentation in Biomedical Informatics (3 credits)

Research (3 credits)

BIOINF 2480 MS Research Project (3 credits)

Elective Courses (14 or more credits)

Electives are chosen by the trainee — which must be approved by the trainee’s advisor — and consist of 2xxx or higher level courses that address trainee’s educational and career goals. Courses that are not listed below can also be chosen with approval from the trainee’s advisor.

BIOINF 2016 Foundations of Translational Bioinformatics (3 credits)

BIOINF 2018 Introduction to R Programming for Scientific Research (3 credits)

BIOINF 2021 Human-Computer Interaction and Evaluation (3 credits)

BIOINF 2103 Design & Analysis of Biomarker Study (3 credits)

BIOINF 2117 Applied Clinical Informatics (3 credits)

BIOINF 2124 Principles of Global Health Informatics (3 credits)

BIOINF 2125 Informatics and Industry (1 credit)

BIOINF 2129 Internship in Global Health Informatics (3 credits)

BIOINF 2990 Master’s Independent Study

Additional Requirements

Biomedical Informatics Colloquium (0 credit): The colloquium will showcase presentations from DBMI researchers and invited speakers from across campus and beyond. It will meet weekly for one hour during the Fall and Spring terms. Minimum 75% attendance is required of all trainees.

Instruction in the Responsible Conduct of Research: This Web-based set of instructions and evaluation modules may be accessed at http://www.ctsi.pitt.edu/RCR/index.shtml.

Attendance at and participation in the Department Biomedical Informatics’ invited lectures, symposia, conferences, etc, e.g., and the Annual Training Program Retreat.

Curriculum

All required courses must be taken for a letter grade, with the exception of the Journal Clubs, Biomedical Informatics Colloquiums and some Independent and/or Research Studies (to be determined by faculty advisors). A minimum grade of “B” is required in all graduate courses. The Master’s committee may waive course requirements that have been satisfied through prior university-level study, in accordance with the Committee on Graduate Studies guidelines. A trainee must comply with the regulations of the Committee on Graduate Studies, as well as those regulations established by the biomedical informatics faculty. We expect that the average full time trainee will complete the degree in two years.

The Master’s degree in Biomedical Informatics requires at least 36 credits that include 23 credits of required core coursework, 10 credits of electives (includes any transfer credits), and 3 credits of research.

Essential Series

The essential series courses should be taken during the first semester, if needed.

BIOINF 2012: Problem-Oriented Programming (3 credits)

[Strongly recommended for trainees who have little or no programming experience]

BIOINF 2013: Introduction to Patient Care and Clinical Environments (3 credits)

[Strongly recommended for trainees who do not have U.S. clinical exposure and are likely to pursue health informatics]

BIOINF 2015: Mathematics for Biomedical Informatics (3 credits)

[Strongly recommended for trainees who have past course work in fewer than 2 of the following 3 areas: calculus, linear algebra, and probability]

Biology: TBA or check with Training Program Coordinator

[Strongly recommended for trainees who have no biological training and are likely to purse bioinformatics]

Foundation Series (9 required core credits)

BIOINF 2011: Foundations of Clinical and Public Health Informatics (3 credits)

BIOINF 2051: Foundations of Bioinformatics (3 courses)

BIOINF 2118: Statistical Foundations of Biomedical Informatics (3 credits)

Research Methods Series (6 required core credits)

Two of the follows courses:

BIOINF 2119: Probabilistic Methods in Artificial Intelligence (3 credits)

BIOINF 2120: Symbolic Methods in Artificial Intelligence (3 credits)

BIOINF 2121: Human Computer Interaction and Evaluation Methods (3 credits)

Research Skills Series (8 required core credits)

BIOINF 2032: Biomedical Informatics Journal Club (1 credit) - Fall Term

BIOINF 2032: Biomedical Informatics Journal Club (1 credit) - Spring Term

BIOINF 2014: Biomedical Informatics Project Course

BIOINF 2134: Publication and Presentation in Biomedical Informatics (3 credits)

Elective Courses (3 or more credits)

BIOINF 2016: Foundations of Translational Bioinformatics (3 credits)

BIOINF 2017: Clinical Research Informatics (3 credits)

BIOINF 2052 (CMPBIO 2030): Introduction to Computational Structural Biology (3 credits)

BIOINF 2060 (CMPBIO 2070): Computational Genomics (3 credits)

BIOINF 2101: Probabilistic Methods for Computer-based Decision Support (3 credits)

BIOINF 2110: Concepts of Software Project Engineering in Health Care (3 credits)

BIOINF 2111: Cognitive Studies for Health Informatics (3 credits)

BIOINF 2113: Realtime Outbreak and Disease Surveillance (3 credits)

BIOINF 2117: Applied Medical Informatics (2 credits)

BIOINF 2124: Principles of Global Health Informatics (3 credits)

BIOINF 2125: Informatics and Industry (1 credit)

BIOINF 2990: Masters Independent Study (1-6 credits)

BIOINF 2993: Masters Directed Study (1-6 credits)

Research (3 required credits)

BIOINF 2480: Master’s Project Research (3 credits minimum)

Additional Requirements

Biomedical Informatics Colloquium (0 credit): The colloquium will showcase presentations from DBMI researchers and invited speakers from across campus and beyond. It will meet weekly for one hour during the Fall and Spring terms. Minimum 75% attendance is required of all trainees.

Instruction in the Responsible Conduct of Research: This requirement must be satisfied within the first month of beginning any academic program at the Department Biomedical Informatics through the CITI training modules.

The University of Pittsburgh now requires the completion of CITI training modules for all individuals involved in research. Go to http://www.rcco.pitt.edu/ResearchTrainingRequirements.htm to access the Training for Researchers guidance document. To simplify user access and better track completion of required research courses, we have built a special pathway or portal to access CITI using the current Pitt HSConnect login process. This will allow users and administrators to continue to use the same method to identify which courses have been completed. All new investigators and research team members, including non-Pitt/UPMC investigators, must create an account on the University of Pittsburgh HSConnect site which can be found at: www.hsconnect.pitt.edu. Users must go through the Pitt CITI Access Portal to affiliate with the university as there is no way to directly affiliate with the university from the CITI website. If you completed the CITI training using by selecting UPMC as your participating site, you must still go to the Pitt CITI Access Portal to affiliate with the University of Pittsburgh.

Once you complete the online modules, it is YOUR responsibility to present a copy of your completion certificate to the Training Program Coordinator for your permanent record.

Conflict of Interest: This requirement must be satisfied within the first month of beginning any academic program at the Department Biomedical Informatics through the CITI training modules.

Login to the Superform Web site: https://coi.hs.pitt.edu, using your HS Connect login. Under “Review & File Your COI Forms,” select “University of Pittsburgh Faculty/Researcher Form” or “University of Pittsburgh Designated Administrator/Staff Form” to begin making your disclosure. Print your signature page and present it to the Training Program Coordinator.

Attendance at and participation in the Department Biomedical Informatics’ invited special lectures, symposia, conferences, etc., e.g., The Annual Lindberg Lecture and particularly the Annual Training Program Retreat. Such lectures are considered to be important educational experiences, and introduce trainees to the primary researchers and their work in the field of biomedical informatics.

Comprehensive Exam

Master’s Comprehensive Examination

A key element of the program is a research project with two key deliverables: (1) the writing and submission (to the Training Program, via their master’s project committee) of a paper of publishable quality based upon the research and (2) the completion of an oral examination on its contents (which satisfy the Master’s Comprehensive Examination requirement). The research project is required of master’s and PhD trainees. The research paper is expected to be 20-30 pages double spaced type, inclusive of abstract, figures, tables and references, and to include Objective, Background, Design, Measurements, Results, and Conclusion (or the equivalent, dependent on the specific research focus). There is the strong expectation that trainees will submit their projects for publication to appropriate journals and conferences, such as JAMIA, AMIA, or other respected academic publications in their field of study. All trainees should refer to the Master’s Research Project Requirements below for detailed description of this requirement, including committee, timeline, and deliverables.

Trainees have the option of developing their project into a formal master’s thesis. It is expected that those trainees who choose the thesis option will additionally satisfy all University requirements, including format and submission of copies, for the master’s thesis. For more information, see http://www.pitt.edu/~graduate/regmasters.htmland http://www.pitt.edu/~graduate/dissertation.htmlUniversity policy requires submission of thesis to be in electronic form for the master’s degree, see http://www.pitt.edu/AFShome/g/r/graduate/public/html/etd/

Projects/Thesis

Masters Research Project Requirements

Committee: A master’s project committee will oversee the student’s research progress, including the oral comprehensive examination. Under the guidance of his/her research advisor, a student will choose a topic, convene a committee, develop a proposal, and discuss it with the project committee in a proposal meeting before the end of the first term of the second year of full-time master’s study.A minimum of three faculty members will form the committee. Two committee members must be TP Core Faculty members, including the chair. These requirements also apply to the thesis option. The trainee must provide the TP Coordinator the names of the committee members.

The trainee should provide committee members and the TP Coordinator with at least 3 weeks advance notice of both the proposal meeting and the final oral presentation.The student is also responsible for providing each committee member a copy of his/her paper two weeks in advance of his/her oral presentation. The oral presentation is open to all faculty and trainees, and an announcement of oral presentations will be sent out by the TP Coordinator. The committee will remain after all other attendees leave the room to address specific issues with the student. A final copy of the master’s project or thesis must be turned into the TP Coordinator. (Note: Final certification of completion of the Masters requirements will not be given until the TP Coordinator receives the hardcopy of the research project.)

Timeline and Milestones: Students are generally expected to complete all requirements for the master’s research project by the end of the second year of full-time master’s study. The oral presentation fulfills the University’s comprehensive examination requirement for the master’s degree. These requirements also apply to the thesis option

Content and Structure: Requirements for content are identical for both the Master’s Research Project and the Master’s Thesis. It is expected that the majority of Master’s projects and theses will be either research papers or theory formation papers, therefore requirements for both are described below.*

Research paper: Full length papers presenting original hypotheses and findings.

Style:

Abstract: Less than 250 words, structured according to Objective, Design, Measurements, Results, and Conclusion.
Length: 20-30 pages double spaced type, inclusive of abstract, figures, tables and references.

Outline:

Introduction - A short statement that presents the purpose of the paper.
Background - Motivate and place the work in context. Subsections might address the significance of the problem being addressed, other approaches to the problem, prior work on the approach being reported.
Research question or hypothesis.
Methods - Subsections might include selection of sites and subjects, intervention, measurements, analysis.
Results
Discussion - Subsections might address significance, limitations, future work.
Conclusion - Short statement of findings and implications.
References

Review criteria:

The reported work is original and data have not been reported previously.
The background and references acknowledge how the findings build on, extend, agree with, or refute prior work.
The level of detail of the methods permits the reader to understand how to reproduce the results.
The results are presented non-ambiguously.
The discussion clarifies the generalizability and limits of the findings.
The findings represent a significant addition to the knowledge-base of the field of medical informatics.

Model Formulation Paper: Full-length papers proposing a model, frame work, or technique. The paper should clarify and validate the proposal through an example.

Style:

Abstract: Less than 250 words, structured according to Objective, Design, Measurements, Results, and Conclusion.
Length: 20-30 pages double spaced type, inclusive of abstract, figures, tables and references.

Outline:

Introduction - A short statement that presents the purpose of the paper.
Background - Motivate and place the work in context. Subsections might address the significance of the problem being addressed, other approaches to the problem, prior work on the approach being reported.
Formulation process
Model description
Validation through example
Discussion - Subsections might address significance, limitations, future work.
Conclusion - Short summary of the model and implications.
References

Review criteria:

The model is original and the validation has not been reported previously.
The background and references acknowledge how the proposal builds on, extends, agrees with, or refutes prior work.
The formulation process is specified in sufficient detail to permit the reader to reproduce the results.
The model definition is clear enough that the reader can apply it to their work.
The validation example and discussion clarify the generalizability and limits of the model.
The model addresses a problem that is significant to the field of medical informatics.

*From the Journal of the American Medical Informatics Association Instructions for Authors

Master’s Oral Examination

Successful completion of the oral examination on the research project satisfies the Master’s comprehensive examination requirement of the University (see Regulations Governing Graduate Study at the University of Pittsburgh). Final certification of completion of the Master’s degree requires submission of an electronic copy of the research project (or, if trainee opts to do so, the formal Master’s thesis) to the Program Coordinator.

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