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Transformational Technologies for
Biology, Medicine, and Health
Honors 222C & MEBI 498A, Spring, 2013

Assignment Calendar: (will be updated throughout the quarter)

Week of Topic Reading assignments (required post to board) Homeworks, exams
April 1

Intro & Motivation

Tues: (none)
Thurs: Text Chpt 2, thru p. 60 (thru sect 2.2.7), and "Meaningful use": Blumenthal 2010. Optionally, look the rest of chpt 2 and at Jha, 2010.
April 8 Notes & Patients
Tues:Delbanco et al., 2012
Thurs: Text, Chpt 12, sects 1-3 and Pratt et al., 2006;
Project #1, part a, due Wed, April 10.
April 15 PHRs and policy issues: Tues:.Halamka, 2008:Early Experiences with PHRs.
Thurs: Ohm, 2009; broken promises of privacy; thru p. 1731 only
April 22 Medical Imaging Tues: No reading
Thurs: Text, Chpt 9 thru 9.5.3 with some skimming.
Project #1 all remaining parts due Tues
April 29 Medical imaging Tues: Text, Chpt 18, most of sections 1 and 2, plus Kobashi and Shapiro, 1995.
Thurs: No reading
Project #2 due Thurs
Catalyst Exam #1: May 5-6
May 6

Bio-Informatics & Synthetic biology

Tues: Text, chpt 22 (entire) and Van T'Veer, 2002, gene profiling.
Thurs: Adventures in Synthetic BIology; also Endy, 2005 Guest lecture: Bryan Bartley
May 13 Synthetic biology & Personal Genomics Tues: Demir et al., 2010, BioPAX
Thurs: Ng,Venter, 2009; & The Ethics of Synthetic Biology (exec summary only, pp. 1 - 18)
Guest lecturers: Nikhil Gopal and Margo Bergman

Project 3 checkpoint 1 (Monday, noon)
Project 3 checkpoint 2 (Friday, 5pm)

May 20 BioInformatics & the Physiome Tues: Hunter, 2003
Thurs: Text, chpt 15 (thru sect 15.4.2 only)
Guest lecturers: Greg A. and Rebecca H.
Project #3 due Friday, 5pm
May 27 Public Health Informatics Tues: Mandl 2004, Syndromic surveillance & Gestelaand
Thurs: CDC case study (see email)
June 3 Final review & Decision making under uncertainty Tues: Ginsberg et al., 2009, & Overhage, 2008.
Thurs: No reading

Project #4 due Friday,
June 7.

Finals week     Catalyst Exam #2: Mon-Wed

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

Shortliffe, EH & Cimino, JC (2006). Biomedical Informatics: Computer applications in health care and biomedicine (3rd edition). Springer.

I would recommend purchasing this if you are interested in the field broadly; however, it is NOT required for this course. The selected readings, both in the text and from other sources are available from the course Eres pages. (Please note: there are more readings on this site than those that are actually assigned!)

General expectations:

My goals for the assignments in the course are to (a) teach you something about the breadth of biomedical informatics research and (b) give you hands-on experience with some of the systems used in the field. I will teach the course largely as a research seminar -- this means that parts of most classes will include student-led discussion.

I expect you to be adult learners. I am assuming you want to be in class, and that you want to learn the material I'm advertising to teach. I will therefore also expect to learn from you -- teaching and learning work best when it is a two-way street.

Reading assignments:

In addition to (obviously) reading these prior to class, I also expect you to be able to discuss them in class. In some cases, this may require multiple readings; it certainly means that you must think about what you read, and perhaps taking some notes to help you offer discussion points and ideas during class. To help with this task, I am requiring you to write and post at least a couple of sentences or thoughts about each assigned reading to the class message board (Catalyst GoPost).

Thus, for each reading assignment listed above, please tell me (and your peers) something new that you learned from the reading, and optionally a follow-up question. You should certainly read other students' posts, and you may also reply or respond to these postings. (As specified on the grading page, class participation is 12% of your final grade.)


The two exams will be conducted as Catalyst on-line (& open book) exams, and will therefore occur outside of the classroom. They will be primarily short-answer questions, and will be designed to evaluate your understanding of the broader concepts and over-arching themes in biomedical & health informatics. There will be no cummulative, final exam, nor any requirements during finals week.


There are four projects, and each is described in a separate web page: see Project #1 , Project #2 , Project #3 and Project #4. Projects are to be handed in electronically, via the course catalyst drop box.

Last Updated:
March 2013

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