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Handouts, Assignments and Readings

MEBI 530, Fall 2013
Introduction to Biomedical and Health Informatics

Assignment Calendar: (will be updated throughout the quarter)

Week of Topic Reading assignments due this day
Homework due this day
Week 1
    Oct 1
Diversity of Motivations and Backgrounds in BHI

  Oct 3

Week 2
    Oct 8

Biomedical Context of BHI
Chapter 1 of Shortliffe and Cimino ("S&C"), p. 3-45

Gawande chapter

S&C Series preface and Preface to the 3rd edition
 2 page essay

    Oct 10
PLEASE ATTEND ITHS TOOLS & TECHNOLOGIES MEETING - South Lake Union Bldg C - Smith Auditorium 3-4:30pm
1. “Genomes for All” (Church)
2. Chapter “The Case of the Red Leg” from “Complications” (Gawande) 
3. Health Care as a Human Right video (Paul Farmer) (one man's perspective on global health)
(* optional 
Kidder chapter)

Week 3
    Oct 15
Evolution of Concepts in BHI
Ch. 2 “Creation of a New Discipline” M Collen.
Ch. 2 “Mapping Medical Informatics Research” (Eggers, Huang, Chen et al)
Altman: “2010 Translational bioinformatics year in review” (2011)
1-2 page discussion - trending topics
    Oct 17
Evolution of Concepts in BHI, cont.
Tables of contents from each:
1) Compare the approaches to organizing BHI from the readings.  Come to class with notes on observations for discussion

2) Go to :

Pick 2 keywords of your choice, enter values using pubmed per the instructions.
Week 4
Oct 22
Driving Problems, Forces & Politics of Importance to BHI
S&C 2006:
  • Chapter 22 “Bioinformatics” Altman (S&C 2006)
  • Chapter 12 “Electronic Health Record Systems” Tang and McDonald (S&C 2006)
  • Chapter 15 “Public Health Informatics and the Health Information Infrastructure” Yasnoff,  O’Carroll, and Friede (S&C 2006)
1 page outline (and 1st draft essay)

Reminder: 1st essay draft due 10/25/13!

Oct 24

Week 5
Oct 29
Driving Problems, Forces & Politics of Importance to BHI

Please read:

1)      CTSA RFA -

Read only:

-          Part 2 section I " Funding Opportunity Description" and

-          Section 4 - subsection: "Informatics Coordination and Research Data Security"

2)      Overview of Meaningful Use -

3)      One other journal publication or news article of your choice pertaining to “driving problems, forces and politics” that seek to employ biomedical and health informatics (BHI)

Provide at least 2 insights for discussion, contrasting perspectives of those looking toward BHI for solutions (readings above) to that of BHI as a discipline looking outward (readings from last week)
Oct 31
Evaluating and Assessing
R tutorial

Week 5
Nov 5
Evaluating and Assessing
Using Pubmed, identify one quantitative, and one qualitative evaluation study of some informatics resource or intervention. One should measure sensitivity/specificity against a gold standard.

Plus review of the following (do not read over 50 pages but do familiarize yourself with the chosen document; available in the library if not online. IOM reports can be found at
•    The Computer-Based Patient Record – An Essential Technology for Health Care (IOM 1991 & 1997)
•    To Err is Human – Building a Safer Health System (IOM; 2000)
•    Crossing the Quality Chasm – A New Health System for the 21st Century (IOM; 2001)
•    Preventing Medication Errors (IOM; 2007)
•    Letter Report. Opportunities for Coordination and Clarity to Advance the National Health Information Agenda: A Brief Assessment of the Office of the National Coordinator for Health Information Technology:
•    Who Will Keep the Public Healthy? Educating Public Health Professionals for the 21st Century (2003)
•    Catalyzing Inquiry at the Interface of Computing and Biology (2005) (select 1-2 chapters)
•    Publications from the Leapfrog Group
•    The CDC Framework for Program Evaluation in Public Health
Pubmed articles
–Read and summarize the article’s approach, methodology, and findings
–We will discuss in class on Tuesday

IOM report:
Write responses to these points , drawing from your readings:
  • To what extent is it possible to be certain how effective a medical informatics resource really is?
  • What are the most important criteria of effectiveness?
  • How do different concepts of effectiveness appeal to distinct stakeholders?
Nov 7
Read S&C Chapter 3
Read Friedman and Wyatt, Evaluation Methods in Biomedical Informatics Chapter 8 (handout link shows an incomplete preview)

Nov 12
Decision Making

Nov 14
Decision Making (slides)

Nov 19
Decision Making (slides)
Please read:
1. “Culture Bias in Medicine” in Lynn Payer, Medicine & Culture: Varieties of Treatment in the United States, England, West Germany, and France, Owl Books 1996
2. “The Ideology of Machines: Medical Technology” in Neil Postman,Technopoly:  The Surrender of Culture to Technology, Vintage Press 1993
Treeage "how to" handout, example
  • Choose a decision problem in your domain of interest
  • Create a tree with >10 outcome nodes & >3 chance nodes
  • Define outcome values and probabilities
  • Perform 1-way and 2-way sensitivity analysis on the decision
  • What are the key features of the decision, and how (and in what circumstances) would your decision change based on the sensitivity analysis?
  • Upload your decision tree and a document with your analyses to the Dropbox
Nov 21
Information and computer science (slides)
S&C Chapter 19, 20

Nov 26
Data Standards
Choose one or find another that interests you: - Pick reading on one data standard  - e.g. ICD-9 (see
 - Find examples of data expressed in the standard
 - Post to observations to discussion board:
 (Complexity / Expressivity? Readability?
Class structure / hierarchy? Semantics?)
Dec 3
Medical Imaging
(slides) (Murat Maga lecture materials)
Read S&C Chapter 7 (Standards)
 - skim 7.1-7.3 & 7.6; read 7.4-7.5 in full;
Read Chapter 9 (Imaging);
Install Fiji -  an image processing tool based on ImageJ

Dec 6
Course wrap up

In the above calendar, "Text" refers to the Shortliffe textbook:

“Biomedical Informatics: Computer Applications in Health Care and Biomedicine” 3rd Edition,
Shortliffe and Cimino (2006).

All other reading assignments from the primary literature are listed above.

Reading assignments:

Please read assignments prior to class and come prepared to discuss them in class.  Your participation in class is crucial to forming your ideas, and will contribute to the quality of your assignments and essays.


Please submit homework assignments by noon on the due date via the course CollectIt Dropbox.

Last Updated:
 Dec 3, 2013

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