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CTS 395/CS 295 Introduction to Biomedical Informatics (Fall 2011)

University of Vermont
Center for Clinical and Translational Science

SYLLABUS
(As of 2011-04-01)

CTS 395/CS 295: Introduction to Biomedical Informatics

Fall 2011, 3 Credits

Time: Tuesdays and Thursdays


1:00 PM – 2:15 PM

Format: Lecture and Lab

Location: HSRF 200

Instructors: Indra Neil Sarkar, PhD, MLIS Elizabeth S. Chen, PhD


Given Courtyard, N309 Given Courtyard, N311
802-656-8283 802-656-8286
neil.sarkar@uvm.edu liz.chen@uvm.edu

Office Hours: By appointment

COURSE DESCRIPTION
This survey course provides an overview of the field of biomedical informatics covering
relevant topics in computer science, healthcare, biology, and social science. Particular
emphasis will be given to understanding the organization of information in biomedicine
and healthcare, the effective management of this information using computational
approaches, and the impact of such approaches on biomedical research, education, and
patient care. Discussions of approaches and methods in biomedical informatics will be
complemented with hands-on experience with existing resources and systems, including
those used in biological, clinical, and public health contexts. The final capstone project of
this course will require the in-depth examination, critique, and presentation of a specific
topic in biomedical informatics, ideally within the context of student (biomedical,
healthcare, or computational) interests.

This course has no pre-requisite requirements. No assumptions are made about


computer science or healthcare background; however, some experience with computers
and a high-level familiarity with biomedicine or health care will be useful. This course
does not require any programming knowledge, and it will not teach students how to write
programs.

The course is open to junior/senior level undergraduates, graduate students, and clinical
fellows. Auditors are permitted with specific permission from the instructors, and are
expected to participate in all course activities.

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CTS 395/CS 295 Introduction to Biomedical Informatics (Fall 2011)

GOALS AND LEARNING OBJECTIVES


The goal of this course is for students to gain a broad level understanding of biomedical
informatics. To this end, it is expected that, by the end of the course, students will have
an understanding of biomedical informatics and its relationship to the various aspects of
the healthcare continuum.

Specific learning objectives are thus to:


1. Understand the role of biomedical informatics in the healthcare process
2. Conceptualize how biomedical informatics approaches can be used in the
development of clinical interventions, patient care, and quality assessments
3. Become familiar with the different facets of biomedical informatics, including (but not
limited to) bioinformatics, clinical informatics, imaging informatics, and public health
informatics
4. Identify and, where applicable, quantify advantages and limitations of computational
applications to healthcare

REQUIRED TEXTBOOK / COURSE MATERIALS


Shortliffe EH, Cimino JJ, editors. Biomedical Informatics: Computer Applications in Health
Care and Biomedicine (3rd Edition). New York: Springer; 2006.
ISBN-13: 978-0-387-28986-1

On-line computing/informatics handbook:


http://www.uvm.edu/~eschen/informatics/handbook.html

Additional materials will be distributed as needed via Blackboard: https://bb.vum.edu

GRADING CRITERIA / ATTENDANCE POLICY


The graded elements of the course and their contribution to the final grade are:

Assignments 30%
Midterm Examination 20%
Final Examination 20%
Capstone Project 30%

Specific criteria details:


• Attendance is mandatory and may be taken at a random moment during each lecture.
Un-excused absences will result in up to a 10% deduction in overall course grade.
• Assignments will be available via Blackboard at the end of each lecture. Grades will
be posted in Blackboard.
• Assignments must be turned in physically in class on specified due dates. Late
submissions will not be accepted.
• A single Capstone Project will consist of the form of a submission ready manuscript
(according to JAMIA specification). The project may be submitted anytime before the
final exam. Projects may be done individually or in collaboration with at most two other
students; for group projects all students will receive the same grade.
• Midterm and Final Examinations will comprise of both objective and subjective
questions. The Final Examination will be cumulative. Both examinations will be open-
book and open-notes.

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CTS 395/CS 295 Introduction to Biomedical Informatics (Fall 2011)

SCHEDULE OF TOPICS

Class Date Topic Readings


1 Tue Aug-30 Introduction to Biomedical Informatics Ch. 1, 5
2 Thu Sep-01 Introduction to Biomedical Informatics
3 Tue Sep-06 Biomedical Data Acquisition and Use Ch. 2, 6
4 Thu Sep-08 Biomedical Data Sources
5 Tue Sep-13 Decision Support Principles Ch. 3, 20
6 Thu Sep-15 Decision Support Systems
7 Tue Sep-20 Information Retrieval Ch. 19
8 Thu Sep-22 Information Retrieval Systems
9 Tue Sep-27 Evaluation Ch. 11
10 Thu Sep-29 Evaluation
11 Tue Oct-04 Principles of Standards Ch. 7
12 Thu Oct-06 Standards in Practice
13 Tue Oct-11 Principles of Integration and Interoperability
14 Thu Oct-13 Integration and Interoperability in Practice
15 Tue Oct-18 Management, Finances, & Ethics Ch. 10, 13, 23
16 Thu Oct-20 MIDTERM EXAMINATION
17 Tue Oct-25 No Class (AMIA Annual Symposium)
18 Thu Oct-27 Cognitive Science & Medical Education Ch. 4, 21
19 Tue Nov-01 Natural Language Processing Principles Ch. 8
20 Thu Nov-03 Natural Language Processing Systems
21 Tue Nov-08 Bioinformatics & Imaging Informatics Ch. 22, 9, 18
22 Thu Nov-10 Bioinformatics & Imaging Resources
23 Tue Nov-15 Public Health Informatics Ch. 14, 15
24 Thu Nov-17 Public Health Initiatives
25 Tue Nov-22 No Class (Thanksgiving Recess)
26 Thu Nov-24 No Class (Thanksgiving Recess)
27 Tue Nov-29 Clinical Informatics Ch. 12, 16, 17
28 Thu Dec-01 Electronic Health Records
29 Tue Dec-06 The Future Ch. 24
30 Thu Dec-08 PROJECT PRESENTATIONS
31 (Exam Day) FINAL EXAMINATION

   

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CTS 395/CS 295 Introduction to Biomedical Informatics (Fall 2011)

OTHER IMPORTANT ADMINISTRATIVE DETAILS

Student Learning Accommodations: If you have a formal accommodation plan developed


in conjunction with UVMs ACCESS Office or would like to discuss the supports that you
need in order to learn well in this class, please contact me in the beginning of the semester.
Adaptations and instructional supports are available through consultation with the instructor
and the ACCESS Office.

Details about UVM ACCESS Office can be found at: www.uvm.edu/~access/

UVM’s policy on disability certification and student support:


http://www.uvm.edu/policies/student/disability.pdf

Religious Holidays: Students have the right to practice the religion of their choice. If you
need to miss class to observe a religious holiday, please submit the dates of your absence
to me in writing by the end of the second full week of classes. You will be permitted to make
up work within a mutually agreed-upon time.

Academic Integrity: Academic honesty is expected and will be enforced. The UVM policy
addresses details pertaining to plagiarism, fabrication, collusion, and cheating:
http://www.uvm.edu/policies/student/acadintegrity.pdf

Grade Appeals: If you would like to contest a grade, please follow the procedures outlined
in this policy:
http://www.uvm.edu/policies/student/gradeappeals.pdf

Grading: For information on grading and GPA calculation, go to:


http://www.uvm.edu/academics/catalogue and click on Policies for an A-Z listing.

Code of Student Rights and Responsibilities:


http://www.uvm.edu/policies/student/studentcode.pdf

FERPA Rights Disclosure: The purpose of this policy is to communicate the rights of
students regarding access to, and privacy of their student educational records as provided
for in the Family Educational Rights and Privacy Act (FERPA) of 1974.
http://www.uvm.edu/policies/student/ferpa.pdf

Final Exam Policy: The University final exam policy outlines expectations during final
exams and explains timing and process of examination period.
http://www.uvm.edu/academics/catalogue2011-
12/?Page=allpolicies.php&SM=policymenu.html&policy=Examinations

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