OHSU

Course Catalog

Biomedical Informatics Classes

Course syllabi are subject to change

Anatomy & Physiology
Instructors: Joanne Valerius, MPH, RHIA. Bonnie Altus, MS, RHIA, CHPS
Credits: 0.0
Content: This course covers the basic structure of the body systems, and provides a functional background to those who are new to the healthcare system, and for those that work in healthcare and who use clinical electronic health records. It is an introductory course that utilizes web-based interactive technology along with a textbook. There are no prerequisites, and the course does not include a dissection lab. The course consists of 10 one-week modules and a final exam. Students should allow a minimum of 10 weeks to complete the coursework. Since the course is self-paced, students may take longer to complete the course, but may be contacted by the instructor if regular progress is not being made. Tuition is $300 for OHSU employees, and $500 for non-OHSU employees.
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Syllabus

Bioinformatics and Computational Biology I: Algorithms - BMI 550/650
Instructor: Dr. Shannon McWeeney
Credits: 4.0
Content: The course will be a problem-driven examination of the algorithmic issues in computational biology. The course will provide students with the computational fundamentals underlying the techniques covered. Students will be expected to learn basic algorithm principles, basic mathematical and statistical proofs, and molecular biology. The emphasis is on algorithm development and application to biological problems, particularly those from functional genomics studies. Topics will include: Mapping (Genetic linkage maps, physical maps), Sequencing (Whole genome sequencing: shotgun approaches and ESTs), Sequence analysis (multiple sequence alignment, fragment assembly, EST assembly, genome annotation, algorithmic side of gene finding and BLAST). Students will be evaluated on written assignments and a programming project.
Note: 4 credits includes 1 credit Lab
Prerequisite: None.
Offering: On Campus: Fall
Syllabus

Bioinformatics and Computational Biology II: Statistical Methods - BMI 551/651
Instructor: Dr. Shannon McWeeney
Credits: 4.0
Content: This course will be a problem-driven examination of the quantitative issues in computational biology. The course will provide students with the statistical fundamentals underlying the techniques covered. Topics will include applications involving MCMC Models, Maximum Likelihood, Random Walks, Hidden Markov Models, Estimating Genealogical Relationships and Networks. Students will be evaluated on written assignments and a programming project.
Note: 4 credits includes 1 credit Lab
Prerequisite: Non-BMI students require instructor's permission
Offering: On Campus: Winter
Syllabus

Bioinformatics Programming and Scripting - BMI 565/656
Instructor: Dr. Michael Mooney
Credits: 3.0
Content: The purpose of this course is to equip research scientists with computational skills necessary to create and automate tools to analyze biological data.  The course is divided into four sub-topics: python programming, scripting in unix, biopython library, bioinformatics workflows.  Python will be used used to solve simple to sophisticated programming problems and to review general computational language paradigms such as problem abstraction, data types, file I/O, iteration, functions, and objects.  There will also be an emphasis on writing unix operating system shell scripts to automate repetitive tasks and connect disparate bioinformatics tools using files and pipes.  In addition, students will learn to access public repositories to perform basic bioinformatics tasks such as annotating gene products, sequence searching, and functional queries. This course is designed to be a first year requirement for students in the Bioinformatics and Computational Biology graduate program in Biomedical Informatics. Open to other students with consent of instructor.
Prerequisite: Background must include an introductory programming class including concepts such as variables, loops, I/O, methods, and algorithms.
Offering: On Campus: Fall
Syllabus

Biological Modeling and Simulation - BMI 558/658
Instructor: Arie Baratt
Credits: 3.0
Content: Overall focus on developing and interpreting computational models of biological systems. An overview of sound model design, implementation, testing and prediction will be presented applying to various scales of biological details (ecological, extra-cellular, intra-cellular). 
Prerequisite: Some programming experience, calculus (or instructor permission) and a desire to investigate biology.
Offering: Spring
Syllabus

Business of Healthcare Informatics- BMI 519/619
Instructor: John Kenagy
Credits: 3.0
Content: The goal of this course is to provide skills and knowledge in the area of business practices relating to Healthcare Information Technology. This includes departmental design and management, capital and operating budgeting, the art of the budget planning process, infrastructure design and strategic planning. Also included in this class is the process of defining system requirement, determination of return on investment, delivery modes (ASP vs. in-house), evaluation of vendors, vendor selection, contractual matters, risk analysis, project management, implementation and support strategies. Within this discussion, the pros and cons of "buy vs. build" will be evaluated. The various types of information systems will be discussed. This will include enterprise systems, developmental systems, data warehouse and decision support systems. It will also include challenges presented by various regulatory agencies and laws that have been enacted. One intent of this class is to address many of the Core Competencies of the HIMSS Certified Professional in Healthcare Information and Management System exam.
Prerequisite: BMI 510/610.
Offering: Online: Summer
Syllabus


Capstone: Internship
- BMI 590
Instructor: Varies
Credits: 6.0
Content: A two-term professional work experience with a sponsoring organization. The goal of the internship is to bring together theory, application and current practice in the field of informatics. MBI students will submit a 10-15 page written paper at the end of the second internship term, and present a final report at a DMICE Informatics Conference (on-campus) or remotely (online).
Prerequisite: Interest Form, Resume, Advisor Assignment Form, Course Contract, Project Plan, Education Contract with sponsor, consent of Internship Coordinator. All documents must be submitted prior to the beginning of the Capstone: Internship term. Allow 10 weeks for this process.

Capstone Project- BMI 581
Instructor: TBD
Credits: 6.0
Content: A two to three-term capstone project in biomedical informatics is a non-independent project that will be performed under the close supervision of the capstone advisor. Project possibilities include, but are not limited to: developing a project that fits into a larger framework, systematic review, piece of an ongoing research project, substantial background literature review, assisting in grant writing, curriculum revision, or project with an IT organization, such as ITG. For more information, see the Capstone Project Requirements.
Prerequisite:BMI 570, Consent of instructor, Advisor Assignment Form, proposal outline.

Capstone Project Prep - BMI 580
Instructor: TBD
Credits: 1.0
Content: Students will prepare a written capstone proposal containing a one-page abstract and several pages of the essential details of the proposed capstone project. The proposal must be approved by the capstone advisor in order to enroll in BMI 581 Capstone Project.
Prerequisite:
BMI 570, Consent of instructor. Available only to students admitted prior to Fall 2009.

Clinical Information Systems- BMI 512/612
Instructor: Vishnu Mohan
Credits: 3.0
Content: An in-depth study fo the basic concepts surrounding clinical information systems, with emphasis on electronic health records - terminology and standards, clinical configuration, user interface design, computerized physician order entry, clinical decision support, and clinical reporting. The course then focuses on the practical application of these concepts, including implementation, clinical workflow, privacy and security, certification, medical device integration, and community health information exchange; includes guest lecturers presenting real-world case studies.
Prerequisite: BMI 510/610.
Offering: Online: Fall, Spring
Syllabus

Clinical Research Informatics- BMI 523/623
Instructor: Judith R. Logan, M.D., M.S.
Credits: 3.0
Content: This class will introduce the student to the principles of clinical research informatics. Topics include the design of clinical research, clinical trial administration, good clinical data management, clinical trial registration and publication, subject recruitment, use of administrative databases, registries and electronic health records in research, practice-based research networks, standards in terminology and messaging for clinical research, and research collaboration.
Prerequisite: None
Offering: Online: Fall
Syllabus

Computational Genetics -BMI 559/659
Instructor: Shannon McWeeney, PhD
Credits: 3.0
Content: This course will cover the foundation and principles of molecular genetics and population genetics along with the corresponding techniques used to study them. Emphasis will be given to the biological interpretation of the data types that result from current experimental methods.
Prerequisite: Open to admitted BMI students or permission of the instructor
Offering: On Campus: Fall
Syllabus

Computational Medicine- BMI 563/663
Instructor: Kemal Sonmez, Ph.D. & Shannon McWeeney, Ph.D
Credits: 3.0
Content: The goal of the course will be to review the computational approaches behind the basic science and the technology driving personalized medicine and develop an understanding of the successes and the computational/statistical challenges of the new translational technologies. We will also discuss the computational challenges and opportunities regarding the economical, ethical and regulatory issues, which are core to its large-scale adoption. The Topics will be covered in a manner that will make the content accessible to both bioinformatics and clinical informatics students. Specific case studies will involve cancer and cardiovascular disease.
Prerequisite: Graduate level standing
Offering:Spring - odd years only
Syllabus

Computer Networks- BMI 542/642
Instructor: Justin Fletcher, PhD
Credits: 3.0
Content: An in-depth look at computer networks including communications protocols for the Internet and computer security. An opportunity will be provided to work with common networking gear and to examine network traffic. By the end of the course, students will understand the basics of how the internet operates and is standardized, as well as considerations for health care.
Prerequisite: No prerequisite, but prior completion of BMI 540 suggested.
Offering: Online: Spring
Note: Enrollment limited to admitted Biomedical Informatics students.
Syllabus

Consumer Health Informatics- BMI 520/620
Instructor: Sue Woods
Credits: 3.0
Content: This course focuses on the intersection between consumers, information technologies and health care. We explore the design, use and impact of emerging technologies that aim to engage consumers to participate in their health and health care. Concepts discussed arise from various informatics disciplines as well as health communication, behavioral science, quality improvement, psychology and public health. We will review trends, opportunities and challenges in consumer-facing health information technology, taking the perspective of various stakeholders. Topics include: U.S. trends; information quality; access and usage; clinical integration; online peers; and prevention and chronic illness care.
Prerequisite
: BMI 510/610
Note: Enrollment limited to admitted Biomedical Informatics students.
Offering: Online: Winter
Online Syllabus

Databases- BMI 544/644
Instructor: Dr. Judith Logan, 3.0 credits.
Content: An in-depth look at databases and database management systems. Topics covered will include data modeling, hierarchical and relational databases, query languages (SQL), database optimization, and OLAP and data warehousing.
Prerequisite: No prerequisite, but prior completion of BMI 540 suggested.
Offering: On Campus: Winter; Online: Winter, Summer
Note: Enrollment limited to admitted Biomedical Informatics students.
Syllabus

Design and Evaluation in Health Informatics- BMI 560/660
Instructor: Dr. Vishnu Mohan
Credits: 3.0
Content: Research and development projects in the broad field of biomedical informatics can take many forms, from field studies that improve understanding of the tasks and information needs of users, to development projects that design, build, and deploy information systems, to studies that assess the impact of information systems on health care processes and outcomes. This course provides an overview of the concepts, vocabularies, and strategies needed to design and evaluate projects in biomedical informatics, including a breadth of methodologies drawn from qualitative research, quantitative research, and software engineering. This is a required course and is recommended for students in their first year of the program.
Prerequisite: PHPM 524 or BSTA 511/611, and working knowledge of Excel or consent of instructor.
Offering
: Online: Winter
Syllabus

Electronic Health Record Laboratory Course- BMI 513
Instructor: Vishnu Mohan MD MBI FACP
Credits: 3.0
Content: This course introduces the student to an electronic health record, and familiarizes students with the clinical informatics operating environment. This is a practical, lab oriented course, and will allow students to understand the complex interactions and features that make up a modern clinical information system. (limit of 10 students per class)
Prerequisite: Successful completion of BMI 512
Offering: Online: Summer, Winter
Syllabus

Ethical, Legal, and Social Issues in Biomedical Informatics- BMI 515/615
Instructor: Joanne Valerius, MPH, RHIA
Credits: 2.0-3.0
Content: The goal of this course is to introduce and sensitize students to ethical, legal, and social issues arising in the use of computer-based technology and information systems in the delivery of health care. Topics will include the protection of confidentiality and privacy in an electronic environment, implications for the use of telemedicine and decision-support tools in diagnosis and treatment, and the implications of electronic communication of the physician-patient relationship. The approach will include the analysis of actual situations and case studies. This course meets the ethics requirement for biomedical informatics students in the School of Medicine Graduate Program.
Prerequisite: None
Note: Enrollment limited to admitted Biomedical Informatics students.
Offering: Online: Spring
Syllabus

Managing Ethics in Biomedical Informatics - BMI 576
Instructor: Joanne Valerius, PhD, Melissa Haendel, PhD
Credits: 3.0
Content: Analysis and synthesis of legal and ethical issues and the role of the Health Information Administrator will be covered in this course. AHIMA Code of Ethics and HIPAA legislation are emphasized. Emphasis is on the student's ability to analyze requests for information using critical thinking skills and applying laws is essential. Students will have opportunities to recreate forms to be inclusive of HIPAA law. Students will compare issues of paper based and electronic health records related to confidentiality and data security. Students will develop and present presentations on course content. (For matriculates of Summer 2014 and later)
Prerequisite: None
Offering: Online: Spring
Syllabus

Evidence-Based Medicine - BMI 536/636
Instructor: Dr. Robert Lowe
Credits: 3.0
Content: This hybrid course provides a rigorous introduction to the principles of evidence-based medicine (EBM). It begins with an overview of how to frame an answerable clinical question and then find the best evidence to answer it. The major categories of questions that arise in clinical practice - treatment, diagnosis, harm (etiology), and prognosis - are each covered, with instruction on what is the best type of evidence to answer questions, how to find that evidence, and how to apply it to a given patient. This is followed by units on summarizing evidence (e.g., through systematic reviews and meta-analysis), putting evidence into practice (e.g., implementing clinical practice guidelines), and the limitations of the EBM approach. Some pre-campus coursework is required. See syllabus for details.
Prerequisite: BMI 510/610
Offering: Hybrid: Fall (odd years only)
Syllabus

Health Information Privacy and Security - BMI 549/649
Instructor: Justin Fletcher, PhD
Credits: 3.0
Content: This course focuses on the privacy and security issues associated with health care information and basic elements of computer security.
Prerequisite: Open to admitted BMI students or permission of the instructor
Offering: Online: Winter
Syllabus

Healthcare Quality - BMI 537/637
Instructor: Dr. David Dorr
Credits: 3.0
Content: This course covers methods for measuring, managing and improving the quality of health care. A general overview of the health care system in the United States and beyond is followed by the quality challenges and issues in these systems. Students are also taught the principles of quality improvement and are expected to be able to apply them in practical settings. Current national efforts in performance measures, financial incentives and quality are also covered. The hybrid version of the course includes pre-campus reading assignments (see hybrid syllabus for details).
Prerequisite: None
Offering: Online: Spring
Online Syllabus

Human Computer Interaction in Biomedicine - BMI 548/648
Instructor: Staff
Credits: 3.0
Content: This hybrid course will provide an overview of the principles and tools of HCI design and evaluation techniques. It will begin with 6-8 weeks of directed readings with small assignments or quizzes followed by one week on campus and then completion of a project. The on-campus portion of the course will have lectures in the morning and lab sessions in the afternoon, for 5 days. Topics to be covered include: Principles of good interface design, The iterative process of design, Surveying techniques, Discount usability testing, Cognitive processes affecting usability, Think-aloud protocols, Physiological processes that affect usability, Eye-tracking techniques, Quantitative evaluative measures, and Research topics in HCI. Some pre-campus coursework is required.
Prerequisite: None
Offering: Fall Term Hybrid Course
Syllabus

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Independent Study- BMI 502/602
Instructor: Varies
Credits:
Varies
Prerequisite: Completed 50X/60X form

Information Retrieval- BMI 514/614
Instructor: Dr. William Hersh
Credits: 3.0
Content: An introduction to text information retrieval in health and biomedicine. After an introduction of models and knowledge-based information, the course covers state-of-the-art approaches to on-line content, indexing, retrieval and evaluation methods. The course then continues with research topics in information retrieval, including automated indexing and retrieval, user interfaces and digital libraries.
Prerequisite: BMI 510/610.
Offering: On Campus: Spring; Online: Spring
Syllabus

Introduction to Biomedical and Health Informatics- BMI 510/610
Instructor: Dr. William Hersh
Credits: 3.0
Content: An introduction to the fundamental principles of biomedical informatics, the field concerned with the acquisition, storage, and use of information in health and biomedicine. The course begins with a basic introduction to health and biomedicine as well as computing concepts. It then surveys aspects of electronic health records, decision support systems, standards, security and confidentiality, evidence-based medicine, information retrieval, bioinformatics, public health informatics, imaging informatics, nursing informatics and consumer health informatics.
Prerequisite: None.
Offering: On Campus: Fall; Online: Fall, Winter, Spring, Summer
Online Syllabus
Hybrid Syllabus

Introduction to Computer Science with Java Programming- BMI 5/640
Instructor: Dr. Justin Fletcher
Credits: 3.0
Content: An introduction to computer science focusing on computer representation and storage of data, structured programming, object-oriented programming, algorithms, software engineering and the Java programming language on a UNIX platform. Students must demonstrate knowledge of basic structured programming techniques for admission to the class.
Prerequisite: Prior college-level computer programming course and successful completion of a pretest.
Offering: On Campus: Fall; Online: Fall
Note: Enrollment limited to admitted Biomedical Informatics students who have completed the introduction to computer programming prerequisite.
Syllabus

Introduction to Programming
Instructor: Lisa Vingara
Credits: 0.0
Content:This non-credit, online course will introduce the beginning programmer to programming structure and design, creating a solid foundation for all types of programming. The emphasis will be on procedural programming and control structures, although exercises will be in Java. The course is self-paced. You may begin it at any time and proceed at any pace as long as you complete the lessons in order and within one year. Students with little or no programming experience should expect that a minimum of 10 weeks will be needed to complete the course. The course fulfills the prerequisite for BMI 540 and BMI 565.
Syllabus

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Managing Clinical Classification and Reimbursement Systems - BMI 584
Instructor: Joanne Valerius, MPH, RHIA
Credits: 3.0
Content: This course will address the case studies and applications that focus on the analysis and synthesis of clinical classification system and reimbursement methodologies affecting the role of the Health Information Manager. Students will examine coding compliance and ethical behavior and the effects on revenue issues. Use of software from AHIMA virtual lab is included. Emphasis on ability to process cases in workbook. Group and individual assignments expected.
Prerequisite: Working knowledge of ICD-9 or consent of instructor
Offering: Online: Spring
Syllabus

Managing Information Governance - BMI 582
Instructor: Joanne Valerius, MPH, RHIA
Credits: 3.0
Content: Analysis of healthcare data management theories focusing on the role of the Health Information Manager will be covered in this course. Managing processes for health data structure and content for compliance with standards, regulations, and accreditation is covered. Developing strategies for changing from a paper-based to electronic record is practiced.
Prerequisite: None
Offering: Online: Fall
Syllabus

Managing Professional Practice and Practicum - BMI 588
Instructor: Joanne Valerius, MPH, RHIA
Credits: 3.0
Content:The capstone course provides the student with opportunities to synthesize the coursework learned in this program and to prepare for the transition from student to practicing professional at the Health Information Administrator level. As part of the final project for this course students will articulate a personal philosophy of quality of health information services. Requirements for this course include a 40-hour minimum professional practice experience (PPE) including a written research report.
Prerequisite: Consent of instructor
Syllabus

Medical Decision Making - BMI 538/638
Instructor: Dr. Karen Eden
Credits: 3.0
Content: This course introduces the student to decision analysis (modeling of decisions). Given uncertain information and limited resources, students will learn to model uncertainty and expected outcomes of various decisions. Course will cover Bayesian theory, decision trees, patient utilities, quality of life and cost related to health outcomes. Students will apply decision analysis techniques in addressing real world problems using software (by TreeAge, Inc.) and participate in online discussion of decision analyses in the medical literature.
Prerequisite: Ability to complete basic algebra problems and knowledge of probability are necessary for this course. If you have questions, please email the instructor, Karen Eden, .
Offering: Online: Winter
Syllabus

Medical Terminology/Pharmacotherapy
Instructor:
Joanne Valerius, MPH, RHIA
Credits: 0.0
Content:This course is non-credit and will be taught online by Joanne Valerius. You may begin it at any time and proceed at any pace as long as you complete the lessons in order prior to the start of your program. It fulfills the Medical Terminology and Pharmacology prerequisites for the Graduate Certificate in Biomedical Informatics Health Information Management (HIM) Track. Tuition is $500.
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Syllabus

Mentored Teaching Prep- BMI 654
Instructor: TBA.
Credits: 1.0
Content: Development of contract with mentor for teaching experience. Decisions will be made regarding lectures, deadlines, scope and topics to be covered. Prepare lesson plans, course materials with Mentor (syllabus, calendar, lectures).
Prerequisite: Doctoral student status

Mentored Teaching- BMI 655
Instructor: TBA.
Credits: 3.0
Content: Students teach a subject area course under the mentorship of a faculty member.
Prerequisite: Doctoral student status, BMI 654

Organizational Behavior and Management- BMI 517/617
Instructor: Dr. Joan Ash, Dr. Justin Fletcher
Credits: 3.0
Content: The most important functions of managers in an organization include understanding and motivating individuals and organizing structural systems within which they can work in a productive manner. This course will review the concepts, issues and practices of organizational behavior at the individual, group and organizational levels. Students will practice applying these concepts in simulated situations to improve personal effectiveness in groups or organizations. At the individual level, topics will include perception, decision-making, values, attitudes, job satisfaction, and motivation. The group level topics are work teams, communication, leadership, power and politics, conflict and negotiation. Organizational level topics include organizational structure, work design, human resources policies, organizational culture and change. The hybrid version of the course requires some pre-campus reading. See the hybrid course syllabus for details.
Prerequisite: None.
Offering: Online: Summer, Winter; Hybrid Course: Summer (even years only)
Online Syllabus
Hybrid Course Syllabus

Practice of Health Care - BMI 530/630
Instructor: Dr. Paul Gorman
Credits: 3.0
Content: This course introduces the biomedical informatics student to clinical practice, including the underlying biology and manifestations of selected disease states, the information gathering and reasoning processes used to detect, understand and treat diseases, the health professionals who provide and support care and the clinical settings in which care occurs. In addition to class time, students will observe clinicians caring for patients in real world settings. Clinicians are exempt from taking this class. Students in the master's and PhD programs (Medical Informatics track) will need to substitute a different 3-credit class in its place.
Prerequisite: None
Offering: On Campus: Fall; Online: Fall
Syllabus

Practicum: Biomedical Informatics- BMI 509/609
Instructor: TBA
Credits: 1.0 - 3.0
Content: A practical hands-on experience in an operational biomedical informatics setting at OHSU, a local health software vendor, or a hospital/health system.
Prerequisite: Consent of Internship Coordinator.

Project Management in Informatics- BMI 518/618
Instructor: TBD
Credits: 3.0
Content: The goal of this course is to introduce students to managing biomedical informatics projects. Students will learn the principles of project management, including planning, scheduling, monitoring, and reporting, will develop written presentations, and will become facile with project management software. Students will be required to complete a group project in an operational informatics setting, presenting the results in written form. Enrollment limited to admitted Biomedical Informatics students.
Prerequisite: None.
Offering: Online: Spring
Syllabus

Public Health Informatics- BMI 521/621
Instructor: JA Magnuson
Credits: 3.0
Content: Recent events underscore the need for a strong public health information infrastructure. Public Health Informatics is the study of how public health information is generated, collected, transferred, and shared. This course is designed to introduce both biomedical informatics and public health students to public health informatics. Course topics will include the information needs of public health professionals; barriers and requirements of a public health information infrastructure; data and process standards; electronic health records; electronic data exchange, including security issues; data registries and sources; evidence-based public health and community health assessment; public health informatics tools, such as GIS; public health reporting and surveillance, including communicable disease, environmental, syndromic, and bioterrorism surveillance.
Prerequisite: None
Offering: Online: Summer
Syllabus

Qualitative Research Methods- BMI 561/661
Instructor: Dr. Joan Ash
Credits: 3.0
Content: Qualitative research methods are used to address why, what, how questions and often triangulated with quantitative methods. This hybrid course will be useful for students taking Organizational Behavior and Management in Informatics when writing their cases. Informaticians who evaluate or conduct research within organizations will find this course a useful foundation when considering data gathering options. Required reading prior to first on-campus session: Crabtree, Miller textbook (see textbook list for details).
Prerequisite: BMI 510/610
Note: Enrollment limited to admitted Biomedical Informatics students.
Offering: On Campus: Hybrid Course, June
Syllabus

Quantitative Research Methods- BMI 562/662
Instructor: Dr. Annette Totten
Credits: 3.0
Content: The aim of this course is to help students apply the knowledge gained in previous biostatistics courses to quantitative research problems in biomedical informatics. Students are expected to have a sound understanding of basic techniques in biostatistics including descriptive statistics, t-tests, chi-squared, ANOVA, use of contingency tables, correlation and regression analysis, non-parametric methods and modeling. Each week, we will begin with a research question from the informatics literature (or a student's own research). We will identify appropriate research designs, generate hypotheses (if appropriate), select appropriate test statistics, and use software to analyze the data. At the end of the term, we will have covered ten of the most commonly used statistical techniques in the recent informatics literature.
Upon completion of this course, students should be able to:

  1. Generate study designs and hypothesis for common research questions in medical informatics
  2. Given a research question and a data set, analyze the data and provide results
  3. Provide an interpretation of data analysis that is easily understood by a non-statistician.
  4. Critique (and suggest alternatives to) study designs and analyses found in the informatics literature.

Prerequisite: (PHPM 524 or Biostats I & II) and BMI 560 Or consent of instructor.
Offering: Varies. See current Hybrid Schedule on the Class Information page
Syllabus

Reading and Conference - BMI 505/605
Instructor: TBA
Credits: 1.0
Content: This is a journal club style course in which students are required to present a key paper or research method in their particular field of research.

Readings in Bioinformatics and Computational Biology - BMI 553/653
Instructor: Dr.Beth Wilmot
Credits: 1.0
Content: This is a seminar style course requiring significant student participation and will address new and emerging technologies and/or methodologies.
Prerequisite: 550 and 551
Offering: On Campus: Spring
Syllabus

Research in Bioinformatics and Computational Biology- BMI 552/652
Instructor: Eilis Boudreau
Credits: 3.0
Content: In this research course, participating faculty will meet in the first week to discuss their research interests and areas in which they are willing to supervise enrolled students. Students will work independently with the research mentor (or mentors) throughout the quarter. Research presentations will be given at the end of the quarter by all students.
Prerequisite: None
Offering: On Campus: Spring
Syllabus

Scientific Writing and Communication for Informatics Students - BMI 570/670
Instructor: Kathryn Pyle
Credits: 3.0
Content: The focus of this course is technical writing and communication. Students will draft abstracts and papers; write for their courses and theses; and learn about writing for publication in scientific journals and grant proposals. Topics also include bibliographic database searching and presentations and posters for scientific meetings. Students will complete and present both individual and group writing projects. Students are encouraged to take this course early in their programs prior to beginning their capstones, theses or dissertations.
Prerequisite: None
Note: Enrollment limited to 16 admitted Biomedical Informatics students. Course offered on a Pass/Fail basis.Registration priority given to master's and PhD students.
Offering: Online: Fall, Spring
Syllabus

Seminar - BMI 507/607
Instructor: Varies
Credits: 1.0 - 4.0
Content: Special topics in biomedical informatics organized by a group of students or faculty.
Prerequisites: Varies
Note: Course offered on a Pass/No Pass basis.
Offering: Online: TBA
Syllabus

Software Engineering - BMI 546/646
Instructor: Dr. Aaron Cohen
Credits: 3.0
Content: This course covers the basic principles of software engineering geared towards providing students with a solid understanding of the process of producing quality software systems on time and on budget. The main activities in software process models are covered in detail, including: proposal creation, requirements gathering and specification, architecture design, software development methodologies, verification and testing, quality management and maintenance. Students will be expected to demonstrate their mastery of the material by the creation of written documentation for several of these main activities on a hypothetical software project of their choice, as well as by answering homework questions based on assigned reading and passing written exams.
Prerequisite: BMI 540/640 or consent of instructor.
Offering: On Campus: Spring
Syllabus

Standards and Interoperability - BMI 516/616
Instructor: Dr. Judy Logan, Harry Solomon, Interoperability Architect, GE Healthcare
Credits: 3.0
Content: This course will explore the details of healthcare information technology (HIT) interoperability and standards. The evolution of technology in healthcare, along with the impact on clinical information systems, will be studied. The benefits of integrating healthcare information systems will be investigated, as will the challenges of integrating systems across disparate organizations, healthcare disciplines, and technologies.  The value proposition of a standards-based approach to integration will be presented.  Students will learn the process of HIT integration projects, and how that parallels the development process of interoperability standards.  The course will present an in depth look at standards critical to HIT interoperability – HL7 v2, HL7 v3 RIM, CDA, and SNOMED – and at the use of those standards in national regulations and industry-wide efforts such as IHE.  Students will gain experience in navigating through standards documents and tools.  Students will utilize the skills and knowledge gained to design a standards-based interoperability project addressing a real-world need.
Prerequisite:
Students must bring laptop to class.
Offering:
Hybrid: Summer
Syllabus

Symposium - BMI 657
Instructor: TBA
Credits: 3.0
Content: State-of-the-art literature synthesis in an area of research from which the student will be questioned and graded during a student symposium. Student symposia will be scheduled during several weeks during the quarter and each student presentation can last no longer than 20 minutes.
Prerequisite: Doctoral student status

Systems Biology - BMI 556/656
Instructor:Dr. Kemal Sönmez
Credits:3.0
Content:This course addresses design principles behind biological mechanisms as modeled by networks, such as robustness, speed, and cost optimization through examples from transcription regulation, signal transduction, and developmental networks. We will study network motifs from a systems and evolutionary optimization point of view, and analyze specific examples of networks. Secondly, we will cover analysis of networks as rule rewriting systems and Petri nets and their equivalence. We will develop a framework for stochastic simulation as well as graph-based analyses of pathway networks. The course will include a brief primer on linear algebra, control theory, and statistics as they relate to the topics covered.
Prerequisite:BMI 550 and PHPM 525, equivalent computational biology and statistics preparation, or consent of instructor
Offering:On Campus: Spring, even years only
Syllabus

Theory and Methods in Informatics - BMI 589/689
Instructor:Dr. Joan Ash
Credits:2.0
Content:This class will meet weekly to review and assess a selection of theories and research/evaluation methods used in other disciplines that hold promise for informatics. Examples include diffusion of innovations theory, the technology acceptance model, complexity theory, rapid ethnographic assessment, etc. Each student will be responsible for selecting one theory or method as a paper and presentation topic.
Prerequisite: Master's students will be able to take the course with the instructor's permission.
Offering: TBD
Syllabus

Thesis/Dissertation - BMI 503/603 (Instructor TBA)

Note: The information included in this catalog was accurate at the time of publication. Information described in this catalog may change without notice. Not all courses are offered each academic year and faculty assignments may change.