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.

Required CoursePak is available for a small fee in the Health Sciences Rotunda Copy Center.

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. Every week on Tuesday an Article of the Week will be assigned for reading. Articles of the week will usually contain very advanced topics and some time during the Thursday lecture will be devoted to the discussion of them.

Class Participation: Each class 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. Short written analyses will be assigned weekly for some of the discussion material.

Weekly Assingments : You will have a homework due almost every week. The homeworks 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 designing a therapeutic intervention on an existing system or a synthetic system for a technological applications. 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 at the start of class or lab on the date specified on this website, and can be turned in as paper in class or electronically by email. Because solutions will be posted immediately, no late reports will be accepted, so please 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. Each student may be allowed one "academic emergency" per quarter.
You may 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. You also must acknowledge the person(s) that collaborated with you on the solution. Please quote any material that you copy directly, and acknowledge the source of material that you rewrite in your own words. Cheating/plagiarism is not tolerated.
Class attendance and participation is strongly encouraged. Feedback and suggestions about the class will be highly appreciated. You will be responsible for the materials covered in class. Normally, lecture slides will be posted on this site immediately after class.
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.