Biomedical Informatics (BIOINF) Courses

Fall Term, 2008 – subject to change

(as of July 1, 2008)

BIOINF 2011
Introduction to Biomedical Informatics (ISSP 2015 / INFSCI 2901/HRS 2429) (4 Credits)
A survey of fundamental concepts and activities on information technology applied to health care. Topics include computer-based medical records, knowledge-based systems, telehealth, decision theory and decision support, human-computer interfaces, systems integration, the digital library, and educational applications. Department-specific applications such as pathology, radiology, psychiatry and intensive care are also discussed.
Instructor: Shyam Visweswaran, MD, PhD
Days/Times: Mondays, 10:00 a.m. to 12:30 p.m. and Wednesdays, 10:00 a.m. to 11:30 a.m.
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: None
Recitations: None
Expected class size: 20-25
This course is usually offered in the fall term. Special permission from instructor is required for this course.

BIOINF 2012
Problem-Oriented Programming in Medical Informatics (ISSP 2062) (3 credits)
This course is designed to extend students’ programming abilities through review of current program design and coding techniques, including fourth-generation languages, the Unified Modeling Language (UML), Object-oriented Programming and Extreme Programming. The course includes a strong practical programming component based on the Python language that includes in-class laboratories, weekly practical programming problems, and midterm and final programming projects. Programming assignments are drawn from areas relevant to medical informatics such as structured text and image processing, network communications, database management, natural language processing, expert systems, etc. Through the course, students learn to understand the programming process at a practical level and gain the ability to independently create useful software tools.
Instructor: Brian E. Chapman, PhD
Days/Times: Thursdays, 9:00 a.m. to 12:00 noon.
Location: Parkvale Building, Room 222, 200 Meyran Avenue
Prerequisites: One course in introductory Programming, or equivalent experience.
Recitations: None
Expected class size: 8-16
This course is usually offered in the fall term. Special permission from instructor is required for this course.

BIOINF 2013
Introduction to Patient Care and Clinical Environments (3 credits; optional for U.S. trained clinicians)
http://courseweb.pitt.edu
This course is designed to introduce biomedical informatics students who have no significant clinical experience in the U.S. to the various clinical environments in which health care providers create, manage, and use clinical information. No previous clinical experience is assumed. Students will be expected to attend lectures and will spend a significant portion of their time examining and reporting on different clinical settings throughout the semester.
Instructor: Natalia Morone, MD and Steven Handler, MD
Days/Times: Thursdays, 1:00 p.m. to 4:00 p.m.
Location: Parkvale Building, Room M184, 200 Meyran Avenue and various clinical areas
Prerequisites: None
Recitations: None
Expected class size: 10-12
This course is offered in the fall term. Special permission from instructor is required for this course.

Biomedical Informatics Colloquium (Lecture Series) (This is not a formal course.)
This course meets once each week for one hour. The current research of Biomedical Informatics faculty and senior fellows will be presented.
Instructor: Various speakers
Days/Times: Fridays,11:00 a.m. to 12:00 noon
Location: Parkvale Building, M-184 VALE, 200 Meyran Avenue
Prerequisites: None
Recitations: None
Expected class size: 35
This course is offered in both fall and spring terms.

BIOINF 2033
Introduction to Research in Biomedical Informatics (1 Credit)
Students will explore the fundamentals of basic and applied research in biomedical informatics, with instructor-lead readings and discussions on a wide range of topics, including important aspects of experimental design, modes of scientific inference, science as a way of knowing, ethical issues of scientific research, special issues in the information age, the value of awareness of the impact of culturalism in multidisciplinary research, the purpose and value of the peer-review process, and the role of informatics in medical scientific research.
Instructor: Brian Chapman, PhD
Days/Times: Tuesdays, 1:00 p.m. to 2:00 p.m.
Location: Parkvale Building, M-184 VALE, 200 Meyran Avenue
Prerequisites: This course is open only to students in the Biomedical Informatics Training Program of the Department of Biomedical Informatics.
Recitations: None
Expected class size: 25
This course is offered in the fall term. Special permission from instructor is required for this course.

BIOINF 2051
Introduction to Bioinformatics (ISSP 2081) (3 Credits)
Provides an introduction to selected topics of bioinformatics also known as computational biology. In this course, the difficult computational problems involving different types of biological information are identified using case studies from current literature. Emphasis is on genomic aspects of computational biology with some overview of proteomics and structural aspects. The course is structured as a seminar course intending to draw students into participating in discussions related to both problems and existing solutions.
Instructor: Vanathi Gopalakrishnan, PhD
Days/Times: Mondays and Wednesdays 12:30 p.m. to 2:00 p.m.
Location: Parkvale Building, M-184 VALE, 200 Meyran Avenue
Prerequisites: An introductory biology course and an undergraduate mathematics course.
Recitations: none
Expected class size: 10
This course is offered in the fall term. Special permission from instructor is required for this course.

BIOINF 2053
Sequence Analysis Laboratory (3 Credits)
This course will give students hands-on experience with sequence analysis software by involvement in an intensive workshop offered by the Pittsburgh Supercomputing Center. In addition, students will work on a study project directed by the instructor that will enable them to apply bioinformatics techniques to a challenging biomedical problem.
Instructor: Vanathi Gopalakrishnan, PhD
Days/Times: TBA
Location: M-184 VALE, 200 Meyran Avenue & The Pittsburgh Supercomputing Center
Prerequisites: BIOINF 2051 Introduction to Biomedical Informatics.
Recitations: none
Expected class size: 3
This course is offered in the summer term. Special permission from instructor is required for this course.

BIOINF 2058
Bayes & Empirical Computational Bayes Methods (BIOST 2064) (3 Credits)
This course provides the students with an understanding of both the theory and practice with regard to the EM algorithm, Markov-chain, sampling techniques, importance sampling, and the solution of decision trees. Students gain hands-on experience programming with S-Plus.
Instructor: Roger S. Day, Sc.D.
Days/Times: Tuesdays and Thursdays, 11:30 a.m. – 12:55 p.m.
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: BIOST 2063
Recitations: none
Expected class size: 6-10
This course is offered in the fall term, every even year. Special permission from instructor is required for this course.

BIOINF 2059
Algorithms for Computational & Predictive Biomedicine (3 credits)
This course teaches widely-used computational approaches from disparate fields, specifically, machine learning, signal and image processing, natural language processing and graph theory. Each algorithm will be presented with application to a specific problem in the area of computational biomedicine or predictive medicine. By presenting the most fundamental concepts or algorithms from each of these fields, this course provides the students with the ability to identify the best algorithm or the field approach to solve a biomedicine question at their hand.
Instructor: Madhavi Ganapathiraju, Ph.D.
Days/times: Mondays and Wednesdays, 10:30 a.m. 12:00 p.m.
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: Working knowledge of Calculus, Probability Theory, and Linear Algebra
Recitations: None
Expected class size: 15
This course is offered in the spring term. Special permission from instructor is required for this course.

BIOINF 2082
Bioinformatics Journal Club (1 Credit)
This course meets once each week for one hour. The research being presented will be taken from recent journal papers, specific to the field of bioinformatics and related areas.
Instructor: Various speakers
Days/Times: TBA
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: None
Recitations: None
Expected class size: 35
This course is offered in the spring term. Special permission from instructor is required for this course.

BIOINF 2101
Probabilistic Methods for Computer-Based Decision Support (ISSP 2070 / INFSCI 2905) (3 Credits)
This seminar provides an introduction to computational approaches for probabilistic modeling and inference. A particular focus is placed on Bayesian networks, although other probabilistic models also will be studied. Medical applications are emphasized, however, the principles are
general and no medical knowledge is needed to take the course. The course does not require knowledge of a computer programming language.
Instructor: Gregory F. Cooper, MD, PhD
Days/Times: Tuesdays and Thursdays, 1:30 to 3:00 p.m.
Location: Parkvale Building, Room M184, 200 Meyran Avenue
Prerequisites: An understanding of basic probability theory would be helpful, but is not required.
Recitations: None
Expected class size: 15
This course is usually offered in the fall term. Special permission from instructor is required for this course.

BIOINF 2109
The Internet and Health Informatics (NURSP 2087) (3 Credits)
This course is designed to survey applications and technologies for health informatics. Web-based and multimedia approaches will be emphasized. The focus will be on the design, development and evaluation of applications that support training, education and access to health information. The course is taught in a web-enhanced format.
Instructor: Gilan Saadawi, M.D., M.S.
Days/Times: Mondays, 1:00 to 4:00 p.m.
Location: School of Nursing, Rm. 114 Victoria Hall
Prerequisites: None
Recitations: none
Expected class size: 10-12
This course is offered in the spring term, every even year. Special permission from instructor is required for this course.

BIOINF 2110
Concepts of Software Project Engineering in Health Care (HRS 2428) (3 credits)
This course examines how health care organization implement both clinical and financial information systems. The course will study the implementation process and how to integrate systems to create the computerized patient record (CPR). Students will also have the opportunity to learn about the industry-wide implementation data standards and how to manage them.
Instructor: Melissa Saul, M.S.
Days/Times: Mondays and Wednesdays, 5:00-7:55 p.m.
Location: 6048 Forbes Tower.
Prerequisites: No prerequisites.
Recitations: none
Expected class size: 30
This course is offered in the summer term. Special permission from instructor is required for this course. (e-mail mis18@pitt.edu, obtain permission, then obtain signed permission slip from Toni, 8084 Forbes Tower)

BIOINF 2111
Cognitive Studies for Health Informatics (3 credits)
This course is intended to serve as an intensive introduction to Human Information Processing and a survey of its applications to Health Care Informatics. The first four weeks present an overview of the basic architecture of the human information processing system. For each of the last twelve weeks of the course, we alternate classes concentrating on underlying basic cognitive science issues and principles, with classes focusing on how these principles and issues apply in medical informatics domains, such as medical decision support, design of information systems, and computer-based education for health professionals. Students will learn and apply methods for studying cognitive tasks, such as verbal protocol analysis and cognitive modeling.
Instructor: Rebecca S. Crowley, M.D., M.S.
Days/Times: Tuesdays, 9:00-12:00 noon
Location: 304 UPMC Cancer Pavilion.
Prerequisites: No prerequisites.
Recitations: none
Expected class size: 10-12
This course is offered in the spring term, every even year. Special permission from instructor is required for this course.

BIOINF 2112
Methods and Principles of User-Centered Design (3 credits)
This course covers three major topics: ethnographic-based methods for determining system design; principles of human factors and interface design; and usability assessments techniques. These topics will be examined using data and examples from medical-related domains. Students will work in teams to analyze data from pre-existing contextual inquiry (CI) interviews, generate and prototype design ideas using both (CI) data and design principles, and refine the ideas through usability assessments. Additional topics (e.g., computer supported cooperative work, designing for special populations, handheld devices) will be included towards the end of the semester and will be based on class interests. Class format will consist of lectures and student presentations.
Instructor: Valerie Monaco, Ph.D., MHCI
Days/Times: Wednesdays, 9:00 a.m. to 12:00 noon
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: Programming experience or by permission of instructor.
Recitations: none
Expected class size: 6-12
This course is offered in the fall term, every odd year. Special permission from instructor is required for this course.

BIOINF 2113
Realtime Outbreak and Disease Surveillance (3 Credits)
Many countries are constructing real-time public health surveillance systems. This work—which is proceeding in an accelerated manner due to the threats of emerging diseases, bioterrorism, and common infectious diseases—can benefit greatly from the expertise of the medical informatics community.
This course on the theory and practice of outbreak detection will present up-to-the minute information about the theory and practice of real-time public health surveillance. This course will cover key topics ranging from the network level to the application level to the organizational level. Specific topics will include functional requirements (e.g., for data, for analysis, for performance), terminology standards, data models, and messaging standards. We will cover algorithms for the automatic detection of epidemics including natural language processing techniques with an emphasis on methods for validation. The experience gained from field deployments of real-time detection systems in Utah, Ohio, Taiwan, New Jersey, Georgia, the Commonwealth of Pennsylvania and other locations will be presented. There will be demonstrations of a surveillance system in operation.
Instructor: Michael M. Wagner, M.D., Ph.D.
Days/Times: Tuesdays and Thursdays, 3:30 to 5:00 p.m.
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: Introductory statistics course. The course can be followed by anyone with medical, medical informatics, or public health background. Ideally, the student will already understand the basic concepts of ROC curve analysis, sensitivity, specificity, positive predictive value, statistical significance testing.
Recitations: none
Expected class size: 12-25
This course is offered in the spring term, every even year. Special permission from instructor is required for this course

BIOINF 2114
Introduction to Medical Language Processing (3 Credits)
Biomedical informatics applications may be used for decision support, quality assurance, assistance in research studies, and resource allocation. However, much of the information that drives these applications in free-text format and cannot be manipulated by a computer. Natural language processing (NLP) attempts to automatically retrieve, classify, summarize, or extract information from text.
This class will introduce students to NLP in the medical domain with an emphasis on techniques, applications, and evaluation strategies used in medical language processing (MLP). The class will overlap slightly with the NLP class taught by Diane Litman in Computer Science in that we will spend some time learning about the building blocks of NLP, including syntax, semantics, and pragmatics. However, a large portion of the class will focus on NLP topics peculiar to the medical domain and to evaluation techniques.
Instructor: Wendy W. Chapman, Ph.D.
Days/Times: Tuesdays, 9:00 to 11:00 a.m. and Thursdays, 9:00 to 10:00 a.m.
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: BIOINF 2011 Introduction to Biomedical Informatics.
Recitations: none
Expected class size: 15-20
This course is offered in the spring term, every odd year. Special permission from instructor is required for this course.

BIOINF 2131
Practicum in Advanced Biomedical Information Technology (ISSP 2090) (1-6 Credits)
This course is designed for people who want a practical experience in working with advanced information technology in the Center for Biomedical Informatics.
Instructor: Center for Biomedical Informatics Faculty and Staff
Days/Times: TBA
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: Discuss with Instructor
Recitations: None
Expected class size: 20
This course could be offered in any given term — check schedule. Special permission from instructor is required for this course.

BIOINF 2132
Special Topic Seminar in Medical Informatics (3 Credits)
This course is designed for faculty to offer small groups of students a study course on a topic of mutual interest and concern in the faculty member s area of expertise.
Instructor: Center for Biomedical Informatics Faculty (will vary)
Days/Times: TBA
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: Discuss with Instructor
Recitations: None
Expected class size: 20
This course could be offered in any given term — check schedule. Special permission from instructor is required for this course.

BIOINF 2133
Practicum in Advanced Infectious Disease and Public Health Surveillance (Biosurveillance) Technology (1-6 Credits)
This course is designed for people who want a practical experience in working with advanced biosurveillance technology in the realtime outbreak and disease surveillance (RODS) laboratory.
Instructor: Center for Biomedical Informatics Faculty (will vary)
Days/Times: TBA
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: Discuss with Instructor
Recitations: None
Expected class size: 20
This course could be offered in any given term — check schedule. Special permission from instructor is required for this course.

BIOINF 2134
Research Writing Practicum (3 credits)
This course will provide a practical overview of how to write a research manuscript. Students will be required to successfully submit a manuscript for publication in order to complete the course.
Instructor: Rebecca Crowley, MD, MS and Wendy W. Chapman, PhD
Days/Times: Mondays and Fridays, 1:30 to 2:55 p.m.
Location: Shadyside, Cancer Pavilion, Room 308 (Mondays) and Parkvale Building, Room M-184 (Fridays)
Prerequisite: Completed data collection for study in research project with approval of both research advisor and course instructor.
Recitations: None
Expected Class Size: 8
Special permission from instructor is required for this course.

BIOINF 2200
Introduction to Dental Informatics Research (3 Credits)
This course is intended to expose trainees to the breadth and depth of dental and craniofacial research problems. The course will center on the six research areas of the National Institute of Dental and Craniofacial Research: Craniofacial Anomalies & Injuries; Infectious Diseases & Immunity; Neoplastic Diseases; Chronic Diseases; Biomaterials, Biomimetics, & Tissue Engineering; and Clinical, Behavior, & Health Promotion Research. By learning about specific research problems in dentistry, trainees will be able to identify which informatics-related solutions would be most helpful to solve them. In this course, we expect trainees to develop several ideas for their Master’s Thesis or other research projects.
Instructor: Titus K.L. Schleyer, DMD, PhD and Heiko Spallek, PhD
Days/Times: TBA
Location: Salk Hall
Prerequisites: None
Recitations: None
Expected class size: 2-4
This course is offered in fall or spring term (as per instructor decision). Special permission from instructor is required for this course.

BIOINF 2201
Dental Information Systems Infrastructures (3 Credits)
This series of seminars and assignments is centered on the management of large-scale information technology infrastructures, with practical experience provided in management of large user bases, help desk management, systems management, end user training, disaster prevention and recovery, and computer security. The course will emphasize practical exercises within the information systems infrastructure at the School of Dental Medicine. The course also includes several special topics related to dental informatics in academia and industry.
Instructor: Titus K.L. Schleyer, D.MD, PhD and Heiko Spallek, PhD
Days/Times: TBA
Location: Salk Hall
Prerequisites: None
Recitations: None
Expected class size: 2-4
This course is offered in fall or spring term (as per instructor decision). Special permission from instructor is required for this course.

BIOINF 2202
Dental Informatics Seminar (3 Credits)
In this course, students will review current research projects of the Center of Dental Informatics and seminal research in dental/medical informatics. Participants will critically evaluate studies, methodologies, and results. During the course, students will prepare and conduct a joint research project of limited scale and scope resulting in a publishable paper or report. The course also includes other topics of interest for dental informaticians in academic careers.
Instructor: Titus K.L. Schleyer, DMD, PhD and Heiko Spallek, PhD
Days/Times: TBA
Location: Salk Hall
Prerequisites: None
Recitations: None
Expected class size: 2-4
This course is offered in fall or spring term (as per instructor decision). Special permission from instructor is required for this course.

BIOINF 2203
Dental Informatics Masters Thesis Research (3 Credits)
Dental informatics trainees will be expected to register for this mentored research experience with dental informatics faculty while they are working on their research project/thesis. This course emphasizes interdisciplinary projects that integrate several domains. Research topics may include information needs and retrieval, decision support, intelligent agents, computer-based patient records and educational applications. Special emphasis is placed on applying informatics research methods to ongoing research projects at the School of Dental Medicine.
(Note: A Dental Informatics Certificate Program and a Ph.D. Program is planned for the future.)
(Note: For Health Services Research (HSR) concentration, see specific curriculum at http://www.dbmi.pitt.edu/trainingprogram/hsr-ms.html and http://www.icre.pitt.edu/degrees/degrees.html )

BIOINF 2480 (1-6 credits)
Masters Thesis/Project Research

BIOINF 2990 (1-14 credits)
Masters Independent Study

BIOINF 2992
Information in Radiological Imaging (3 credits)
This course provides an introduction to the nature of information in radiological images. Standard clinical techniques will be examined as well as current radiology research topics. Three basic units will be covered: image formation, image postprocessing, and image quality assessment.
Instructor: Brian E. Chapman, Ph.D.
Days/Times: TBA
Location: M-184 VALE, 200 Meyran Avenue
Prerequisites: None
Recitations: None
Expected class size: 20-25
This course is usually offered in the spring term, every odd year. Special permission from the instructor is required for this course

BIOINF 2993 (1-9 Credits)
Masters Directed Study

BIOINF 3990 (1-14 Credits)
Doctoral Independent Study

BIOINF 3995 (1-9 Credits)
Doctoral Directed Study

BIOINF 3998 (3 Credits)
Doctoral Teaching Practicum

BIOINF 3999 (1-9 Credits)
Doctoral Dissertation Research

NOTE: Students registering for Full-time Dissertation Study must register under the School of Medicines Course Number: FTDS 0000 (0 Credits)