Computing for Bioinformatics (810:065), Fall 2007

Time and Place: 2:00 to 3:15 PM Tuesday and Thursday in ITTC 322


Class Email List: Send messages to from your UNI account (let me know other email addesses that you want to use)

Instructor: Mark Fienup (

Office: ITTC 313

Phone: 273-5918 (Home 266-5379)

Office Hours: M 9-11, 1-2; T 9:30-10:45; W 9-10, 1-2; Th 9:30-10:45; F 9-11

Prerequisite: Computer Science II (810:062) and Discrete Structures (810:080)

Required Text: "An Introduction to Bioinformatics Algorithms" by Neil C. Jones and Pavel A. Pevzner,

MIT Press, ISBN-10: 0-262-10106-8 (or ISBN-13: 978-0-262-10106-6)

Course Description: "Intermediate programming with emphasis on bioinformatics. Includes file handling, memory management, multi-threading, B-trees, introduction to dynamic programming including Wunsch-Neddleman and Smith-Waterman algorithms for optimal alignments, exploration of BLAST, FASTA and gapped alignment, substitution matrices." Our text does a great job of bioinformatics algorithms, but we'll need to supplyment it with discussions of file handling and B-trees.

Assignments: The assignments will consist of "pencil-and-paper" exercises, programming assignments, and output analysis using existing Bioinformatics tools on the Internet.

Pedagogic Approach: In class, I'll tend to break up the lecture with active and group learning exercises to aid learning. While this is not formally graded, part (5%) of your grade will be based on your participation on these in-class activities. Students benefit by (1) increased depth of understanding, (2) increased comfort and confidence, (3) increased motivation, and (4) being better prepared to work in groups on the job. This might sound great, but it will require you (and me) to work differently to prepare for class. Before the class, you must read the assigned reading, thought about what I've asked you to think about, etc.; otherwise you won't be able to effectively participate in your group during class.

Grading policy: There will be three tests (including the final). I'll announce tests at least one week in advance to allow you time to prepare. Tentative weighting of course components is:

In-class Work: 5 %

Assignments: 33 %

In-class Test 1: 20 % (~September 27)

In-class Test 2: 20 % (~November 8)

Final: 22 % (Wednesday, December 12 from 1-2:50 PM in ITT 322)

Grades will be assigned based on straight percentages off the top student score. If the top student's score is 92%, then the grading scale will be, i.e., 100-82 A, 81.9-72 B, 71.9-62 C, 61.9-52 D, and below 52 F. Plus and minus grades will be assigned for students near cutoff points.

Special Notice: In compliance with the University of Northern Iowa policy and equal access laws, I am available to discuss appropriate academic accommodations that may be required for students with disabilities. Requests for academic accommodations are to be made during the first three weeks of the semester, except for unusual circumstances, so arrangements can be made. Students are encouraged to register with Student Disability Services, 103 Student Health Center, to verify their eligibility for appropriate accommodations.