Bioen 485 Home Page

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.

Paperless submission and grading: All assignments are turned in using CollectIt, where you will log in using your UWnetID. You will upload all assingments here, and recieve comments from the instructors as well. No one can see your work but you and the instructors. Assignments in .doc, .docx, or .pdf forms are all accepted. Please note due dates and Closing dates (see course policy below).

Reading Assignments: This year, the text book (Physiological Control Systems: Analysis, Simulation and Estimation by Michael C. K. Khoo, New York: IEEE Press, 2001) is recommended but not required since it is only used for part of the class. Several copies of the book will be placed on 24-hour reserve at the UW engineering library. If you prefer, you may purchase it from the UW bookstore or elsewhere.

The remaining readings are from current literature and will be available on-line, including Article of the Week assignments from the current literature that provide examples of how the topics you learn in class can be applied to solve a problem in science or engineering.

Laboratory Assignments: Students will build models to simulate biological problems, and will interpret the results. The models will often be inspired by original research articles that the students read and discuss in class for the “paper of the week.” These may 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, but you will usually need to finish the assignment outside of lab. The computer laboratory for BIOEN 485 is located in BIOE N140. 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. For more details on the grading and expectations of these assignments, see General Expectations on Laboratory Assignments.

Midterm Project: Students will select an example system of deterministic differential equation modeling from a published research article. The project will include 1) a critical review of the literature on the system chosen to describe the contribution of this article to the knowledge base, 2) a computer implementation of the model that reproduces the key figures in the article, and 3) an discussion of whether the published results could be reproduced and what was learned from the implementation that may not have been apparent in the published article. For more details.

Final Design Project: A final design project is required. Students will work in small groups to design a novel computational model to solve a specific bioengineering problem chosen by the group. Students will identify the criteria for the model, design and build a model, and evaluate the success of the model in meeting the criteria.

Reading Discussion Homeworks: For most Tuesdays, an article of the week is assigned the previous Thursday. You must prepare a < 1/2 page analysis on the topic to help you prepare. You will submit these on-line and be often be graded on them. For more details, see discussion assignments and grading.

Class Attendance: While you are required to participate in class discussions most of the time, you are NOT expected or encouraged to come to class or lab when you are sick. We do not take attendance, and all assignments are submitted electronically anyway. We also post all assignments and lecture notes on-line, and are available by email to help you understand material. There should be no reason you need to attend a class, lab or office hour in person if you are infectious with any flu. If you think of something else that will make it easier to continue to participate when infectious, please email Wendy with your suggestion.

Assignments will be graded on ability to perform simulations and analysis, and to evaluate how computational tools add to the understanding of the problem. Below are the maximum points available for each of these items:

Catalyst GradeBook will be used to publish scores. Go to the grade book URL and log in with your UW NetID and password. You can only view your own scores.

Deadlines. All assignments (reading anlaysis, labs, and projects) must be turned via CollectIt, before the start of class (11:00 am) on the date specified on this website (Tuesdays for Readings and Projects, Thursdays for labs, in general.) 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. Check here for an update on where the department has such a resource, or email wendy if this isn't posted yet.

Health, family, and other emergencies. However, 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.

Helping vs Cheating: 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.

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.

Specific outcomes in Bioen 485 and their assessment mechanisms to be used by the department for program assessment are:

(a) An ability to apply knowledge of mathematics, science and engineering This item will be taught in the lectures, labs, reading assignments, discussions, and projects. They will be assessed on their ability to use a mathematical model to answer scientific and engineering questions about a biological system in one of the lab reports.

(c) An ability to design a system, component, or process to meet desired needs. Student’s ability to design a system will be assessed in their final project, in which they identify a bioengineering problem, and design a computational model that will meet this need.

(e) An ability to identify, formulate, and solve engineering problems. This item will be taught in the lectures, labs, and projects. In lab reports, students will be evaluated on their ability to formulate a quantitative model from a conceptual description of a biological system, and to use the model to address a problem of medical or biological relevance.

Additional outcomes and their assessment mechanisms considered of high relevance to ABET criteria by the department for Bioen 485 are:

Those specific outcomes and their assessment mechanisms considered of medium relevance by the department for Bioen 485 are:

(d) teams/ multidisciplinary teams. Students will be evaluated on their ability to work together in small teams for the final design project.

Bioen 485 is designed to introduce quantitative modeling and systems analysis to upper division undergraduates and graduate students. Students integrate the knowledge they learned in computer modeling, mathematics, and physiology, to probe the biological systems behavior.