Course: BIOEN 337 – Mass Transport and Systems Laboratory

Credits: 2

Instructor: Alyssa Taylor

Texts and Supplemental Materials: None.  Readings will be assigned from the mass transport and systems texts in BIOEN 335 and BIOEN 336.  Each lab project will have a handout with background, procedure, and reference to appropriate literature.  Journal articles may be assigned as outside reading to reinforce concepts discussed in lecture and to provide real-world bioengineering context for the lab experiments.

UW Catalog Description: Computational and experimental laboratory exercises to demonstrate time- and space-dependent linear and nonlinear systems with specific emphasis on bioengineering applications.

Instructor Overview:

This course is designed to reinforce and provide in-depth, hands-on exploration of the topics covered in BIOEN 335 (Mass Transport and Kinetics in Biological Systems) and BIOEN 336 (Bioengineering Systems and Control).  Lab projects will involve the analysis and control of linear and nonlinear systems, involving both ODE and PDE solution approaches. Labs will involve practical lab applications in bioengineering such as mass transport, electrical systems, enzyme kinetics and control systems. In addition to wet-lab and instrumentation-based experiments, emphasis will also be placed on computational analysis of the systems and acquired data.  Computational projects will use MATLAB or LabVIEW.

 Prerequisites by Course: BIOEN 327, and STAT 390 or IND E 315.

Corequisites:  Requires concurrent registration with BIOEN 335 and 336.

Prerequisites by Topic: Probability and statistics, differential equations, biotransport I (momentum and heat), linear algebra, computational numerical methods (MATLAB), circuit building.

Required or Elective: Required

Course Schedule:  One three hour formal lab period per week. Students are expected to spend additional time in lab or on analysis (~3 hours per week).

 Computer Use:  Requires word-processing software for preparing lab reports and the term project, and on-line access to communicate via email and download materials from the course web site. Most computational projects will use MATLAB or LabVIEW. Excel or other statistical analysis software may be required for data analysis and plotting. ImageJ (NIH) will be needed for the 1-D diffusion lab and can be downloaded for free.

 Course Outcomes and Assessment:  This course presents, through weekly lab exercises, an opportunity for students to engage in practical exploration of concepts involving mass transport and systems analysis and control. As such, this course addresses certain ABET student learning outcomes at a variety of levels.

 Specific Outcomes: By the end of the course, students should be able to:

  1. Use a model to predict an outcome and carry out experiments to validate predictions.
  2. Use statistics to determine how noise in data affects system analysis.
  3. Implement a feedback controller.
  4. Work effectively in interdisciplinary teams to complete projects.
  5. Document experimental findings.

Outcomes Addressed by this Course:

B.  An ability to design and conduct experiments, as well as analyze and interpret data.

  • Design and conduct an experiment then analyze and interpret the data in order to test model predictions.

This course is entirely lab-based, and students will be required to design and execute experiments on a weekly basis, as well as implement quantitative techniques to analyze and ultimately interpret their results. Student competency will be assessed primarily through an individually-based written report, in which students will use a computational model of 1-D diffusion to generate predictions of concentration profiles and compare those predictions to experimentally-acquired data of 1-D diffusion in a gel. Students need to design the experiment by creating their experimental set-up, decide on time points, etc. and afterwards they conduct the experiment.

D.  An ability to function on multi-disciplinary teams.

  • Work effectively in interdisciplinary teams to complete projects by:
    1. Attending work group sessions
    2. Fulfilling assigned team roles
    3. Contributing to group work effort
    4. Listening to team mates
    5. Cooperating and consulting with team mates.

Most laboratory exercises in this course require that students work in groups of 3-4 (dependent on enrollment). Although all students are from the BIOE major, students by their junior years have often already specialized in a sub-discipline of BIOE. Thus, students are able to work with their peers who may have different interests and strengths. Students must work as a team to collectively design experimental procedures, carry out the experiment, analyze data, interpret data, and generate a lab report. Assessment of this outcome will be conducted through a section of the lab report that describes each team member’s role in the collective effort. Peer evaluations complemented by instructor observations will also be used to assess group work skills via a team work grading rubric.

G.  An ability to communicate effectively.

  • Document experimental findings

Lab modules will require documentation of lab procedures, results, analysis, and conclusions.  Students will practice their written communication skills as they report on the execution and results of each lab module.  One key skill for BIOEN undergraduates to learn is the practice of keeping a lab notebook.  Clear and complete documentation of lab work is required in research labs of universities and non-profit institutions, as well as in industry.  Students will thus be given guidelines on how to keep a proper lab notebook (recognizing that the format of a lab notebook may change depending on the setting).  The ability of students to communicate effectively will be assessed through lab notebooks, which will be checked at the end of each lab session and collected and twice per quarter.

K. An ability to use the techniques, skills, and modern engineering tools necessary for engineering practice (computer and analytical lab equipment).

  • Implement a feedback controller

Labs will involve the use of modern laboratory techniques and equipment (i.e. spectrophotometer), as well as computational tools for both data acquisition and subsequent analysis (i.e. MATLAB and LabVIEW). The ability of students to utilize these tools will be assessed primarily with an individually-based lab report in which students will describe the design and implementation of a PID feedback controller.

M. The capability to apply advanced mathematics (including differential equations and statistics), science, and engineering to solve the problems at the interface of engineering and biology.

  • Use statistics to determine how noise in data affects system analysis

This course involves the use of quantitative mathematical tools to analyze behavior of biological systems.  Labs will involve the use of ordinary and partial differential equations, for instance in the analysis of a glucose transport and conversion model.  Labs require statistical analysis of experimental data sets.  Student competency will be assessed through an individually-based lab report which requires students to statistically analyze the effect of noise in data on enzyme kinetics parameter estimation.

Relationship of course to Program Educational Objectives:

The goal of our B.S. BIOE program is to prepare our graduates for industry, graduate programs, and medicine. BIOEN 337 contributes to this goal by helping to ensure students are able to achieve the following objectives:

Earn advanced degrees and/or obtain employment in bioengineering-related fields, such as medicine, device development, or biotechnology.

Together with BIOEN 335 and BIOEN 336, BIOEN 337 introduces students to fundamentals of mass transport and reaction kinetics as related to biological processes and introduces methods of analysis and control of nonlinear and linear systems in the context of biological/biochemical applications. Execution of labs in teams and an interpretation of their results require an integration of a student’s emerging skills and knowledge in areas such as computational analysis techniques, chemistry, circuit design, control systems, and biology. As such, this course should help students gain technical skills and team-working skills necessary to obtain employment in bioengineering-related fields. They will be required to learn new concepts and skills to complete their projects but they will also realize there is still much left to learn, thus instilling an appreciation for the importance of continuous learning and advanced educational opportunities.

Contribute to responsible development of new technical knowledge.

This class involves hands-on exploration of MATLAB-based analysis, LABVIEW programming, circuit design, wet lab techniques, analytical lab equipment, etc. As such, this course provides students with the tools they can utilize in other settings in order to ultimately contribute to the development of new technical knowledge.  

Take leadership roles in addressing domestic or global bioengineering-related issues.

The lab exercises in this course involve team work. Planning, execution, and analysis of lab projects will give students the opportunity to work collaboratively on a team and to develop both oral and written communication skills. Students will also have the opportunity to hone their leadership skills, both within their team and among their other classmates.

 Topics Covered:

  1. Electrical Analogs (summers, integrators, constant multipliers)
  2. 1-D Diffusion
  3. Soluble Enzyme Kinetics
  4. Effects of experimental noise on parameter estimation; Statistical analysis
  5. Lab Notebook Documentation
  6. Controlled Drug Delivery
  7. PID Feedback Controller

Course Weekly Schedule:

Week Lab Activity Due Assign
1 Course introAnalog Computer I Design Analog Computer Circuit
2 Analog Computer II Circuit design (pre-lab)
3 Analog Computer III Group lab report
4 1-D Diffusion in a Gel 1-D Diffusion lab write-up Individual lab report
5 Soluble Enzyme Lab I Documentation in notebook
6 Soluble Enzyme Lab II Lab notebook check;Soluble enzyme lab report
7 Immobilized Enzymes Documentation in notebook
8 PID Thermal Controller I Lab notebook check;Soluble enzyme lab report
9 PID Controller II Individual lab write-up
10 PID Controller III Individual lab write-up (continued)
Finals Week PID individual lab write-up

*Controlled drug delivery module may replace immobilized enzymes module.

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