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Course Policy

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BIOEN 503, Spring 2012
Systems Bioengineering

Syllabus and Home Page

Course Description

UW General Catalog Course Description: Explores whole-body or organ physiology topics from an engineering perspective. Uses various model systems to elucidate engineering principles such as feedback control and homeostatic regulation. Includes real-world examples, computer modeling, and research design approaches .

Instructor’s Detailed Course Description: BIOEN 503 is a 4 credit class with 2 lectures per week. This course will cover methodological and practical aspects of the application of system analysis, including computational tools, to the solution of outstanding biological and biomedical problems. Class lectures and discussions will be used to provide examples of how systems tools are used in bioengineering research. Homework assignments will focus on the application of the concepts and tools taught in class to the student's individual research projects. The homeworks will build from simple model development to a written proposal for research that integrates models and experiments.

Learning Objectives:

  1. Learn quantitative systems modeling skills and concepts
    • Recast a range of biological problems into quantitative models
    • Choose and apply appropriate analytical or computational systems analysis tools
  2. Evaluate and articulate what value is added by a computational model
    • Learn how to integrate computational and experimental tools
    • Critically evaluate the accuracy of computational models and the certainty of their implications to a biological or biomedical problem.
  3. Learn to design models to aid in research projects
    • Write a proposal for a modeling component of research
    • Learn to critically evaluate research proposals

Topics Covered

  • Types of Systems Models:
    • Linear and Nonlinear Differential Equation Systems
    • Transport Systems (Partial Differential Equations)
  • Systems Analysis Tools
    • Model Building
    • Model Verification Techniques
    • Steady State Solution techniques
    • Mathematical programming (intro to MATLAB and COMSOL)
    • System Identification and Parameter Estimation
  • Project Planning and Proposal Writing
    • Identifying the significance and innovation of a proposed model
    • Planning an integrated approach to quantitative engineering research
    • Communicating a research proposal

Recommended Background

  • multivariate calculus,
  • differential equations,
  • molecular and cellular bioengineering or biology
  • mathematical or computer programming tools.

Class Structure and Organization

Instructor: Wendy Thomas
Office: BIOE N430P
Office Hours: Mondays 2:30 to 3;30 pm
Phone: (206)616-3947
Fax: (206)685-3300

TA: Wilbert Copeland
Office Hours: Thursdays, 11:30a - 12:30p
Room: N461
email: wcopelan@

Class Meeting Times and Location:
Lecture: W & Fr 1:30 - 3:30 PAA A214

Final Exam: please reserve the slot Monday, June 04, 2012,230-420 pm, PAA A214 to participate in a Bioengineering program evaulation, unless you are not in our department. If you cannot make this time, please let Dorian Varga know immediately. However, there is no final exam affecting your grade for the course.

Class Discussion email list : bioen503a_sp12@u. If you are registered for the class, you will automatically be added to the discussion list. The list will be used for me to send you course announcements, and it is your responsibility to check your UWnetID email account on a regular basis for course announcements. You may email the list to discuss class topics, but only if you use your UWnetID email account.

Viewing links on web site: Many of the course documents are not available to the general public and are password protected. You can access them by following instructions to log in with your UW net ID if you are enrolled in the class. If this doesn't work, tell Wendy. Also, most of the readings and assingments are in Adobe Acrobat which you can download for free.

Computer Access: There are two ways to access the Bioengineering Student Computers, which we use for this class.

  • You can log on remotely with a Remote Desktop Connetion (under accessories in Window) to, writing NETID\yourUWnet ID, where NETID is written verbatim and yourUWnetID is replaced by your net ID. (If you have a Mac, you must download and install a remote desktop application: Once it is installed, the process is the same as for Windows.)
  • You can get an access card to room N140; you should already have this is you are a bioengineering student. If you are not, contact Wendy.


Assignments and Grading

Paperless submission and grading: All assignments are turned in using CollectIt. You will download all assignments, upload your work, and recieve comments from the instructors as well. No one can see your work but you and the instructors. Please submit assignments in pdf form, so convert word documents to pdf and scan written assignments. (A scanner is available in the advanced computing lab; BIOE N140).

Discussion Homeworks: During the first six weeks, there will be frequent homeworks assigned for class discussion, that involve reading a scientific paper or solving a pen-and-paper modeling question. These will be graded pass-fail only and are together worth 20% of the grade.

Computational Homeworks: There will be two major homework assignments, worth 15% of the grade each. They will involve solving models computationally, and also analytically, as much as is possible, in order to verify your model. They will also involve answering discussion questions about what is learned from the model. One will be an ODE model in MATLAB and the other a PDE transport model in COMSOL.

Final Project. The final project is worth 50% of the grade, and is done in the last 4 weeks of class. Each student will write a proposal describing incorporation of a systems model into a research project. The proposal must describe the model in detail, including issues of validation, verification, and interpretation, and will include preliminary results that require that you take initial steps of the modeling process. You will participate in a peer review process that should help improve all your projects before the final grading by instructors.

Software. For the numeric portions, the software packages MATLAB and COMSOL will be introduced with tutorials, but at a graduate pace that assumes some previous familiarity with programming or an ability to self teach.This software is available in BIOE N140. For problems concerning the machines in the lab, personal accounts and software, please contact Norbert Berger, 543-9757, Box 355061, at Students are welcome to solve problems using any software tools they chose, but the course instructors strictly provide support for COMSOL and MATLAB only.

Grading. All assignments are graded on a 4.0 scale, with 4 = A, 3 = B, etc. The final course grade is a weighted average of your grades. 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.


Course Policy

Class Attendance: While you are expected to actively participate in class discussions, all materials can be accessed and submitted electronically to accomadate illness and other emergencies.

Deadlines and Emergencies. All assignments (reading anlaysis, labs, and projects) should be turned via CollectIt, by the time and date specified so we can grade them in a timely manner. However, we will be fairly understanding of one or two health, family, academic or research emergencies during the quarter. In this case, contact the instructors prior to the time the assignment is due.

Helping vs Plagiarism. You are encouraged to discuss projects and homework with your fellow students to assist in learning. However, you should never copy directly from something written by another student or a nonscholarly source, including a website. If you copy directly from a scholarly source, place the material in quotes and cite the source material. When you rewrite ideas in your own words, you must also cite the source of material. 

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. 



 Last Updated:
April 20, 2012