FYS 102

FYS 102: Bioinformatics
FYS 102: Bioinformatics
Fall, 2007
Professor: Jessen Havill Phone: 587-6582
Office: Olin 208 E-mail: havill@denison.edu
Web site: http://personal.denison.edu/~havill/      Mailbox: Olin 201
Office hours: Please see the schedule outside my office.


During your lifetime, molecular biologists and geneticists have made amazing medical and biological advances by better understanding the vast information contained in DNA molecules. It seems as though we hear about new breakthroughs every day, from sequencing the genome of a malaria-carrying mosquito to the identification of human genes related to obesity or cancer.
Many of these discoveries were made possible by using computational techniques to organize and analyze DNA, a field called bioinformatics. Without these efficient techniques, or algorithms, processing so much information would be intractable. In this course, we will learn about some of the fundamental problems in understanding genomic data, how scientists derive abstract models of these problems, and then solve them by designing efficient algorithms that can be implemented on a computer.

Required Texts

The Cartoon Guide to Genetics (updated edition) by Larry Gonick and Mark Wheelis
An Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner
Learning Python by Mark Lutz and David Ascher (or another Python reference)
The Bedford Handbook (seventh edition) by Diana Hacker

General Course Outline

  1. What is bioinformatics?

  2. Introduction to genetics and molecular biology

  3. Introduction to algorithms and the Python programming language

  4. Regulatory motif search (branch & bound and greedy algorithms)

  5. Genome rearrangements (greedy and approximation algorithms)

  6. Sequence alignment (dynamic programming and divide & conquer algorithms)

  7. DNA sequencing (graph algorithms)

  8. Pattern matching and database search (data structures)

  9. Gene clustering and evolutionary trees

Web Resources

I will maintain a class web page containing reading assignments, homework assignments, answer keys, examples, and other useful resources. Refer to this page daily for updated information. The class home page can be found at http://personal.denison.edu/~havill/bioinformatics/


In order to be successful in this class, you must take an active role in the learning process by attending class, completing the assigned reading on time, participating in discussions and asking questions, and conscientiously completing assignments.
Attendance. Your attendance is expected at each class meeting, unless your absence is excused for a very good reason. Scheduled absences must be communicated to me well in advance. You are responsible for the content of reading assignments, lectures and handouts, as well as announcements and schedule changes made in class. If you must miss a class, be sure to check with me or another student to get what you missed. Exams will be given in class on the day scheduled and may not be made up.
Reading. It is very important that you finish the assigned reading before coming to class so you will be ready to participate and to ask questions. All reading assignments will be listed on the class web page. Reading in mathematics and computer science is often dense, requiring several passes. It is not enough to scan the reading once without understanding it. You should be prepared to read and study material many times until you grasp it. As you read, you may want to take notes and draw pictures to help you understand the concepts. Be sure to ask questions in class or during office hours if you are unclear about a subject. You can understand even the most difficult concepts with enough perseverance!
Homework. There will be a number of independent assignments given during the semester which will be due in class on the date specified. No late homework assignments will be accepted. Since it will most likely not be obvious how long an assignment might take, you are well advised to start right away. Like other classes at Denison, it is expected that you devote at least 2-3 hours to these assignments for each hour of class time. Your work will be graded on both content and writing style. A correct answer is not very useful if it is not clearly communicated to the reader!

Academic Integrity

The students and faculty of Denison University and the Department of Mathematics and Computer Science are committed to academic integrity and will not tolerate any violation of this principle. Academic honesty, the cornerstone of teaching and learning, lays the foundation for lifelong integrity.
Academic dishonesty is, in most cases, intellectual theft. It includes, but is not limited to, providing or receiving assistance in a manner not authorized by the instructor in the creation of work to be submitted for evaluation. This standard applies to all work ranging from daily homework assignments to major exams. Students must clearly cite any sources consulted - not only for quoted phrases but also for ideas and information that are not common knowledge. Neither ignorance nor carelessness is an acceptable defense in cases of plagiarism. It is the student's responsibility to follow the appropriate format for citations.
As is indicated in Denison's Student Handbook, available through my.denison.edu, instructors must refer every act of academic dishonesty to the Associate Provost, and violations may result in failure in the course, suspension, or expulsion. (For further information, consult the student handbook on the web at http://www.denison.edu/academics/handbook/ar03s02s01.html.)
In this class, you may generally discuss problems with other students in the class, but the work you hand in must be your own. In other words, you may have general conversations about problem strategies, but you must leave these conversations without having written anything down. When it comes time to write your solutions, you must do so on your own. If you have questions, please come see me and I will be happy to help. You are also quite welcome to send me e-mail or call if you would like to discuss an assignment.

Writing Center

The Center is a free resource available to all Denison students. Student writing consultants from many majors help writers one-on-one in all phases of the writing process, from deciphering the assignment, to discussing ideas, to developing an argument, to finalizing a draft. The Center is located on the 4th floor of Barney-Davis Hall; satellite locations are on the third floor of the Library (the Entry level) and the first floor of Fellows near the Computer Lab. Appointments between 4 p.m. and 9 p.m., Sunday through Thursday, can be made in the Barney location by calling 587-JOT1. The satellite locations are drop-in; see http://www.denison.edu/academics/writingcenter/ for hours.


Any student who feels he or she may need an accommodation based on the impact of a disability should contact me privately as soon as possible to discuss his or her specific needs. I rely on the Office of Academic Support to verify the need for reasonable accommodations based on documentation on file in their office.

Grade Determination

The following relative weights will be used to determine your final grade:
3 midterm exams 45%
Writing assignments 35%
Homework assignments 10%
Class participation 10%
There will be no final exam. (Your final research paper will substitute.)
Have a great semester! If you need anything, please let me know.

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On 26 Aug 2007, 17:11.