Bioinformatics Masters Concentration Curriculum

We describe below the Master’s degree curriculum for the Bioinformatics concentration for students who wish to focus on the use of computational methods aimed at solving biological problems. Almost all elements of the proposed curriculum designed to meet the specific needs of students interested in training in bioinformatics exist as courses offered through the Department of Biomedical Informatics, the Department of Computer Science, or other departments within the University that have been admitting informatics trainees to their courses. Research in collaboration with the Center for Computational Biology of the University of Pittsburgh can also be arranged. Also, many rich educational opportunities exist through workshops organized by the Pittsburgh Supercomputing Center.

Entering students are required to have proficiency and/or coursework in computer science or biophysics/biochemistry/genomics. We expect the average full time student will complete the degree in two years, assuming they matriculate with the prerequisites (see above) satisfied. (Note: Up to 6 credits – “B” grade or better – from another institution or department within the University of Pittsburgh can be considered for transfer towards the Biomedical Informatics Master’s degree (bioinformatics concentration). Acceptance of transfer credit must be discussed between student and advisor, and approved by Chair of Curriculum Committee.)

To obtain the PhD degree in Biomedical Informatics, a student must complete a program of study approved by his/her bioinformatics advisor and the Biomedical Informatics faculty. Electives/cognate courses can be chosen in the area of bioinformatics. All other regulations with respect to this doctoral degree will be similar to that described for the Biomedical Informatics doctoral degree in general, except trainees will complete the requirements for the Master’s degree in their respective concentration. Please refer to the Biomedical Informatics Doctoral Curriculum for specifics.

Below is an outline of the Bioinformatics concentration Master’s curriculum (minimum requirement of 36 credits). The curriculum consists of:

Bioinformatics Core (7 credits)

BIOINF 2011: Introduction to Biomedical Informatics (3 credits)

BIOINF 2051: Introduction to Bioinformatics (3 credits)

BIOINF 2082: Bioinformatics Journal Club (1 credit) Revised format will focus on seminal and new literature in the field w/ weekly preparation and critical analysis facilitated by an instructor; required of all students in first year.

Biomedical Informatics Colloquium (0 credit) Revised format will showcase presentations from DBMI researchers and invited speakers from across campus and beyond. Will meet weekly for one hour. Required attendance (75% minimum) for all students.

Computational Competency: Tools and Concepts (minimum 6 credits)

Tools (minimum 3 credits)

BIOINF 2012 Problem-Oriented Programming in Medical Informatics (3 credits) is strongly recommended. An alternative* programming language elective may be substituted, pending approval of advisor.[CG1] Only those students for whom prior experience or other approved forms of demonstrated programming competency proficiency (such as online courses or portfolio development) exist, may seek a waiver of the programming elective.

Concepts (minimum 3 credits)

Database Management (3 credits): INFSCI 2710, HSR 2424, CS 2550 or alternative* approved by advisor.

Data Structures (3 credits): INFSCI 2500 or alternative* approved by advisor.

Algorithms (3 credits): CS 2150 or alternative* approved by advisor.

*Note: alternative courses must be graduate-level courses (having course numbers in the 2000 or 3000 series). Prerequisites may apply.

Bioinformatics Distribution (minimum 9 credits)

BIOINF 2014: Biomedical Informatics Project Course (3 credits)

BIOINF 2052: Introduction to Computational Structural Biology (2 credits)

BIOINF 2053: Sequence Analysis Laboratory (3 credits; includes Pittsburgh Supercomputing Center (PSC) Workshop in August)

BIOINF 2054: Statistical Foundations for Bioinformatics Data Mining (3 credits)

BIOINF 2055: Practical Analysis of High-Throughput Genomic and Proteomic Data Sources (3 Credits)

BIOINF 2056: Bioinformatics of Gene Regulation (3 credits)

BIOINF 2057: Elements of Statistical Learning (3 credits)

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

BIOINF 2134: Research Writing Practicum (2 credits)

Electives (minimum 6 credits)

Student choice which must be approved by the student’s advisor of 2xxx or higher level courses that address student’s educational and career goals. The elective can be met through additional courses chosen from the biomedical informatics distribution list for the general Master’s degree. Students are strongly encouraged to take at least one elective course approved by advisor in an area complementary to their background. Students who are allowed to waive one or more required credits will use additional electives to earn the required 36 total credits for the master’s degree.

Research Methods (8 credits)

Introductory Statistics/Biostatistics (3 credits). The statistics core requirement can be met in a variety of ways. Many of our current students take one or more of the following: Intro to Statistical Methods I (BIOST 2041: 3 credits), Intro to Biostatistics II (BIOST 2042: 2 credits), Statistics in Information Sciences (INFSCI 2060: 3 credits), Statistical Methods I (PSYED 2014: 3 credits), Statistical Methods 2 (PSYED 2015: 3 credits), or Statistical Methods 3 (PSYED 2016: 3 credits). (A waive of this requirement can be requested based on previous coursework in statistics (send e-mail request to tls18@pitt.edu; however, a biostatistics course taken in medical school is typically too brief an experience to justify a waiver.) Those students who must take a course to fulfill this requirement will be strongly urged to do so early in their plan of study.

BIOINF 2033 Introduction to Research in Biomedical Informatics (2 credits). New course being developed as an early structured research experience to be mentored by the student’s research advisor with oversight by Course Coordinator; required of all Master’s and doctoral students in their first year.

BIOINF 2480 Master’s Research Project (3 or more credits) 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. The research project is required of master’s and PhD students. 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 students will submit their projects for publication to appropriate journals and conferences, such as JAMIA, AMIA, Bioinformatics, or other respected academic publications in their field of study. All students should refer to Master’s Research Project Requirements for detailed description of this requirement, including committee, timeline, and deliverables.

Students have the option of developing their project into a formal master’s thesis. It is expected that those students 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.html and http://www.pitt.edu/~graduate/dissertation.html for more information. University policy requires submission of thesis to be in electronic form for the masters degree, see http://www.pitt.edu/AFShome/g/r/graduate/public/html/etd/

Master’s Comprehensive Examination

Successful completion of the oral examination on the research project satisfies the comprehensive examination requirement of the University’s Committee on Graduate Studies (follow procedures outlined in the Master’s Research Project Requirements). Final certification of completion of the Master’s degree requires submission of an electronic copy of the research project (or, if student opts to do so, the formal master’s thesis) to the Program Coordinator.

Additional Requirements

Instruction in the Responsible Conduct of Research: See specific information on Research Practice Fundamentals. This requirement must be satisfied within the first month of beginning any academic program at DBMI.

Attendance at and participation in the Department of Biomedical Informatics’ invited 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, as well as introducing students to primary researchers and their work in the field of Biomedical Informatics.