Links to other pages in this course website:
Syllabus/Home Page contents:
All material on this course website is subject to change without notice.
BIOEN 485/585 (599), Spring 2013
(with ad-hoc honors option for 485)
Syllabus and Home Page
Credits : 4
UW General Catalog Course Description: Introduction to computational and mathematical analysis of biological systems, including control, stochastic and transport systems. Lectures and laboratory sessions emphasize biochemical systems, but also include electrical, mechanical and fluidic systems. Offered jointly with BIOEN 585. Prerequisites: MATH 307 or AMATH 351; AMATH 301; BIOL 200, BIOEN 335.
Prerequisites: while the list of prereqs is long, all junior and senior BioE ugrads have have taken these courses, and interrested students in other departments who lack one or more prereqs are likely to do fine if they have strengths in other areas, so prereqs will frequently be waived. If this applies to you, please discuss your concern with the instructor.
Required for 485 and recommended for 585:
Recommended for 485 and 585:
Instructor’s detailed course description: BIOEN 485/585 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 biological and biomedical problems. This course is intended for students with a background in fields in bioengineering or related fields. The course provides the resources to use MATLAB and COMSOL to solve computational problems, but students are allowed to use alternative computational tools when they have these resources; none of the learning objectives are specific to the tools. Assignments include weekly labs and a final team project in which a model is built to solve a biological or medical problem. Graduate students in 585 will identify research topics for the final team projects and will lead teams of undergraduate students to solve these problems.
Ad-hoc honors: Undergraduate students are encouraged to arrange with Dr. Thomas to take the ad-hoc honors option for this course if they want to learn the graduate level learning objective number 5 below. In practice this means the student will take the same role as the grad students in identifying a project topic. This is only recommended for students already deeply involved in research (grad students, seniors, or juniors who started their research early.) Interested students are encouraged to meet with Dr. Thomas to discuss this option.
Textbooks: The following textbook is recommended for students who have little experience with linear systems, but is not required: “Physiological Control Systems: Analysis, Simulation and Estimation” by Michael C. K. Khoo, New York: IEEE Press, 2001. This book is available electronically to all UW students for free. Required readings include literature articles and instructors’ lecture notes, all posted electronically on the course web.
Learning Objectives: By the end of the course, students should be able to:
Laboratory: There are two laboratory sessions. You should go to the one you are signed up for. However, if you can't, you may go to the other with instructor permission.
Final Oral Presentation: There is no final exam, but we will use the assigned time slot for oral presentation of the final projects.
Computer Use and Access: Students will use mathematical programming in weekly computer labs and thus should be familiar already with at least one such language, such as MATLAB, or at least with a programming language such as C++ or Java. The course materials and instructors will support the use of the programs MATLAB and COMSOL for course assignments, but students are welcome to use alternative mathematical software if they can independently apply it to solve the problems posed. Tutorials for both MATLAB and COMSOL are included, so prior knowledge with these platforms is an advantage but not required. Students will also need to use a word processing program such as word to write reports and projects. There are three ways to access the Bioengineering Student Computers, which we use for this class - log on remotely using your UW net ID, get an access card to room N140, or go during office hours, which are held in the lab. For more more information, download: Detailed Computer Access Instructions. For problems concerning the machines in the lab, personal accounts and software, please contact Norbert Berger, 543-9757, Box 355061, at email@example.com.
Quizzes (10%) will test students’ knowledge of the mathematical tools and problem-solving approaches necessary to succeed in the labs, project, and course objectives.
Weekly Laboratory Assignments (40%) will test students' ability to apply the course material to bioengineering problems. Students will build models to simulate biological problems, and will interpret the results. These may involve some pen-and-paper work, but will be largely solved numerically using the software MATLAB or COMSOL. The submitted solution must includes plots, answers to questions, and code as an appendix, but no formal report is required. The weekly computer lab is designed to get you started on these assignments, but you will need to finish the assignment outside of lab.
Final Project (40%) will test students' ability to integrate the course material to solve a novel bioengineering problem. Students will work in teams to design and use a computational model. The project written and oral reports should include computational solutions, verification of the solutions, validation of the model, and significance of the problem and the solution. While an undergraduate team member (485) may draw on his or her research experience to identify the problem to be solved, the team will usually solve a problem identified by a graduate student (585) or course instructor. The primary role of the undergraduate students is thus the coding, debugging, model verificiation, and/or making of figures. The primary role of the graduate student is to draw on his or her research experience to identify the problem to be solved, and to lead the team to identify and understand the significance of the problem, the most relevant literature, and future or past experimental validation that is outside the scope of the course but would be necessary for publication or other application of the work.
Literature Analysis (10%) will teach students to integrate the course material by discussing specific questions about the paper of the week. Students will prepare for the discussions with a written analysis, and are graded for both preparation and participation in these discussions.
No Final Exam will be administered, but... The final exam slot is used for oral project presentations.
Canvas will be used to post weekly assignments, turn in assignments, track grades, and manage discussions.(Deadlines, Cooperation vs. Plagiarism, Class Attendance, Disability)
Deadlines. All assignments (reading anlaysis, labs, and projects) must be turned via CollectIt, an hour before the start of class (10:00 am) on the date specified (usually Tuesdays for Readings and Projects, Thursdays for labs) Because solutions will be posted on the due date, no late reports can be accepted without prior permission, so turn in everything you were able to accomplish in the allocated time. This means if you have written something in pen and paper, it will need to be scanned.
Health, family, and other emergencies. We will be fairly understanding of one or two health, family, or even academic emergencies during the quarter, if you contact the instructors prior to the time the assignment is due, so we can delay posting the solution for a few days to accomodate your emergency. If you need to do this, please remind the TA that you were given permission by copying the email onto the first page of the assignment. Since assignments are turned in electronically, all lectures are posted on-line, and several quizzes and literature discussions can be dropped without penalty, you are not expected to come to class when you are sick.
Helping vs Cheating: While we do revise the assignments each year, it is considered cheating to consult or copy worked assignments or solutions from any previous year. 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:
Plagiarism. Please place in quotes any material that you copy directly, and reference the source of material when you rewrite ideas in your own words.
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.
Course Outcomes of High Relevance (for 485):
(a) An ability to apply knowledge of mathematics, science and engineering
(c) An ability to design a system, component, or process to meet desired needs.
(e) An ability to identify, formulate, and solve engineering problems.
Relationship of Course to Program Objectives (for 485):
Obtain employment in bioengineering related fields, such as medicine, device development, or biotechnology.
Contribute to responsible development of new technical knowledge.