Bioen 485 Home Page

BIOEN485 is a 4 credit class with lectures and laboratories. This course will cover methodological and practical aspects of the application of system analysis and computational tools to the solution of outstanding biological and biomedical problems. The recent, rapid development of these fields requires an understanding of the mathematical, statistical and computational tools behind such a rapid growth. The advances both in computational power and the understanding of biology have allowed the formulation of increasingly sophisticated and realistic mathematical models of biological systems. This course is intended for students with a background in fields in biology or bioengineering seeking to learn to apply quantitative tools to biological problems.

The material of the course is balanced between theoretical and practical fundamentals and specific case studies, closely integrated with current literature reviews and computer laboratory sessions. Examples from cell biology, metabolism, genomic analysis, protein structure, pharmacokinetics and regulatory networks are presented and will be used to motivate the lectures and closely integrate them with the laboratories.

Equivalent coursework may be substituted for the prerequisites on an individual basis. Please consult the instructor if you are not sure you meet the prerequisites for taking this course.

This book is not yet available at the University Bookstore. You may purchase it on-line from a variety of vendors (eg Amazon), purchase one used, or wait until it is available. Reading material will be handed out in class for the first two weeks.

The course will also be supplemented by readings available on the web. See the Course Schedule for details about the material to read for each week of class.

Class Participation: Most classes will include both lecture and discussion. It is expected that you come to class having read the assigned material and be ready to discuss it. Most Tuesdays, we will discuss an Article of the Week, in which the topics you learn in class will be applied to solve a problem in science or engineering. Short written analyses will be assigned for some of the discussion material. Our discussions and these written assignments will give you practive in reading and evaluating research articles.

Weekly Assingments : You will have a lab assignment due almost every week. These will involve some pen-and-paper work, but will be largely solved numerically using the software MATLAB. We will have a weekly computer lab to get you started on these assignments. The computer laboratory for BIOEN 485 is located in BIOE N140. You should be able to log in with your UW Net ID. For problems concerning the machines in the lab, personal accounts and software, please contact Norbert Berger, 543-9757, Box 355061, at norbert@u.washington.edu.

Projects: The first project will involve reconstruction of a model from the literature and an analysis of what was learned by modeling the system. The second project will be a group project in which you design a new model to solve an engineering, scientific, or educational problem. More detail on both projects is provided elsewhere on the web site.

Assignments will be graded on ability to perform simulations and analysis, and to evaluate how computational tools add to the understanding of the problem. All assignments will be graded on a 0.0 to 4.0 scale, representing a fail to an A. Your final grade will be the weighted average of these according to the following formula:

Class participation will be graded on your active participation in class discussions, not on your attendance. Participation is important to keep you thinking during classes that often cover challenging material. Half of the participation grade will be based on your written analysis on the discussion material. The other half will be based on your oral contribution to the discussion as follows:

All assignments must be turned in before the start of class or lab on the date specified on this website. The m-files must be turned in electronically for grading. A written report with figures and discussion must be turned in as paper unless you obtain permission for electronic submission that week. Because solutions will be posted immediately, no late reports will be accepted, so turn in everything you were able to accomplish in the allocated time. Exceptional circumstances will be considered in the case of emergencies if you contact the professor prior to the time the assignment is due, so we can delay posting of solutions. Each student is allowed one 24 hour "academic emergency" per quarter.
You are encouraged to discuss projects and homework with your fellow students, and even collaborate on the solution, but you may not copy or take credit for another person’s work and you must write your homework, lab or term reports independently. When you help each other, follow these guidelines:
- you cannot give an answer
- you cannot provide code
- you can point out the location or type of mistake in code
- you can teach coding tools
- you can point out the relevant parts of the lecture notes or text.
- you can discuss the pluses and minuses of different approaches
- you can discuss discussion questions in the labs
- Use the type of help given by your instructors as a guideline.
- If you recieve help or collaborate, you must acknowledge the person(s) on your written assignment. You will not be graded down for this.
Please place in quotes any material that you copy directly, and reference the source of material when you rewrite ideas in your own words. Cheating/plagiarism is not tolerated.
Feedback and suggestions about the class will be highly appreciated. Please feel free to email me or talk to me in person.
To request academic accommodations due to a disability, please contact Disabled Student Services, 448 Schmitz, (206) 543-8925 (V/TTY). If you have a letter from Disabled Student Services (DSS) documenting that you have a disability that requires academic accommodations, please present the letter to the instructor so we can discuss the accommodations you might need for the class.