Topics in Computer Science: Bioinformatics (810:188g)

Spring 2005

Time and Place: 8:00 - 9:15 Tuesday and Thursday in Wright 105

Instructor: Mark Fienup (

Office: Wright Hall 321

Phone: 273-5918 (Home 266-5379)

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

Credits: 3 hours (Note: 810:188 counts toward the Foundations area (or as CS elective hours) in the CS majors)

Prerequisite: Computer Science III (810:063) and junior standing

Goals: Bioinformatics is a "hot" career field -- find out what Bioinformatics is all about!

Broadly speaking, bioinformatics is the application of computational techniques to the discovery of knowledge from biological databases. After a brief introduction of the necessary biological background, we'll examine the algorithms, data structures, and tools used in bioinformatics.

Required Text: "Fundamental Concepts of Bioinformatics" by Dan E. Krane and Michael L. Raymer; Benjamin Cummings; 2003; ISBN 0-8053-4633-3

Assignments: Assignments will be a mixture of pencil-and-paper exercises, using existing Bioinformatics tools and databases, writing some programs, and term paper/project.

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 of 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: 24 %

In-class Test 1: 23 % (February 24)

In-class Test 2: 23 % (April 7)

Final: 25 % (Tuesday, May 3 from 8-9:50 AM in Wright 105)

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: The Americans with Disabilities Act of 1990 (ADA) provides protection from discrimination for qualified individuals with disabilities. Students with a disability, who require assistance, will need to contact the Office of Disability Services (ODS) for coordination of academic accommodations. The ODS is located at 213 Student Services Center. Their phone number is 319/273-2676.