BIOEN

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CourseTitle:BIOEN337MassTransportandSystemsLaboratory Instructor:AlyssaTaylor Credits:2 UW Catalog Course Description: Computational and experimental laboratory exercises to demonstrate time and spacedependent linear and nonlinear systems with specific emphasis onbioengineeringapplications. PrerequisitesbyCourse:BIOEN327,andSTAT390orINDE315. Corequisites:RequiresconcurrentregistrationwithBIOEN335and336. Prerequisites by Topic: Probability and statistics, differential equations, biotransport I (momentum and heat), linear algebra, computational numerical methods (MATLAB), circuit building. Overview: This course is designed to reinforce and provide indepth, handson 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 wetlab and instrumentationbased experiments, emphasis will also be placed on computational analysis of the systems and acquireddata.MostcomputationalprojectswilluseMATLABorLabVIEW. Textbooks: None. Reading 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 reinforceconceptsdiscussedinlectureandtoproviderealworldbioengineeringcontextforthe labexperiments. CourseObjectives:Bytheendofthecourse,studentsshouldbeableto: 1. 2. 3. 4. 5. Useamodeltopredictanoutcomeandcarryoutexperimentstovalidatepredictions. Usestatisticstodeterminehownoiseindataaffectssystemanalysis. Implementafeedbackcontroller. Workeffectivelyininterdisciplinaryteamstocompleteprojects. Documentexperimentalfindings.
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TopicsCovered: 1. 2. 3. 4. 5. 6. 7. Week 13 4 56 78 910 ElectricalAnalogs(summers,integrators,constantmultipliers) 1DDiffusion SolubleEnzymeKinetics Effectsofexperimentalnoiseonparameterestimation;Statisticalanalysis LabNotebookDocumentation ControlledDrugDelivery PIDFeedbackController LabTopics Electricalanalogofabiologicalsystem Diffusionina1Dgel Soluble Enzyme Kinetics: Chemical reaction kinetic measurements and leastsquaresparameterestimation ControlledDrugDeliveryfromAlginateSpheres PIDcontroller(thermalcontrol)

CourseSchedule:Onethreehourformallabperiodperweek.Studentsareexpectedtospend additionaltimeinlaboronanalysis(~3hoursperweek). Computer Use: Requires wordprocessing software for preparing lab reports and the term project, and online 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 forthe1Ddiffusionlabandcanbedownloadedforfree. Course Outcomes and Assessment: This course presents, through weekly lab exercises, an opportunityforstudentstoengageinpracticalexplorationofconceptsinvolvingmasstransport andsystemsanalysisandcontrol.Assuch,thiscourseaddressescertainABEToutcomecriteria atavarietyoflevels. Outcomesassessedinthiscourseforprogramevaluationpurposes: (b)Anabilitytodesignandconductexperiments,aswellasanalyzeandinterpretdata. (Useamodeltopredictanoutcomeandcarryoutexperimentstovalidatepredictions.) This course is entirely labbased, 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 individuallybased written report, in which students will use a computational model of 1D
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diffusion to generate predictions of concentration profiles and compare those predictions to experimentallyacquireddataof1Ddiffusioninagel. (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. (Usestatisticstodeterminehownoiseindataaffectssystemanalysis.) Thiscourseinvolvestheuseofquantitativemathematicaltoolstoanalyzebehaviorofbiological 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 experimentaldatasets.Studentcompetencywillbeassessedthroughanindividuallybasedlab report which requires students to statistically analyze the effect of noise in data on enzyme kineticsparameterestimation. (k) An ability to use the techniques, skills and modern engineering tools necessary for engineeringpractice(computerandanalyticallabequipment). (Implementafeedbackcontroller.) 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 individuallybased lab report in which students will describe the designandimplementationofaPIDfeedbackcontroller. (d)Anabilitytofunctiononmultidisciplinaryteams. (Workeffectivelyininterdisciplinaryteamstocompleteprojectsby: a.Attendinggroupworksessions b.Fulfillingassignedteamroles c.Contributingtogroupworkeffort d.Listeningtoteammates e.Cooperatingandconsultingwithteammates.) Mostlaboratoryexercisesinthiscourserequirethatstudentsworkingroupsof34(dependent on enrollment). Although all students are from the BIOEN major, students by their junior years have often already specialized in a subdiscipline of BIOEN. Thus, students are able to work withtheirpeerswhomayhavedifferentinterestsandstrengths.Studentsmustworkasateam 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 members role in the collective effort. Peer evaluations complemented by instructor observations will also be used to assess groupworkskillsviaateamworkgradingrubric. (g)Anabilitytocommunicateeffectively. (Documentexperimentalfindings.) 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
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keepingalabnotebook.Clearandcompletedocumentationoflabworkisrequiredinresearch labsofuniversitiesandnonprofitinstitutions,aswellasinindustry.Studentswillthusbegiven 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 effectivelywillbeassessedthroughlabnotebooks,whichwillbecheckedattheendofeachlab sessionandcollectedandtwiceperquarter. Relationshipofcoursetodepartmentalobjectives: 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 achievethefollowingobjectives:

Pursue educational opportunities and/or employment in bioengineeringrelated fields, such as medicine,devicedevelopment,orbiotechnology. 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 students emerging skills and knowledge in areas such as computational analysistechniques,chemistry,circuitdesign,controlsystems,andbiology.Assuch,thiscourse should help students gain technical skills and teamworking skills necessary to obtain employment in bioengineeringrelated 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. Contributetoresponsibledevelopmentofnewtechnicalknowledge. This class involves handson exploration of MATLABbased analysis, LABVIEW programming, circuit design, wet lab techniques, analytical lab equipment, etc. As such, this course provides studentswiththetoolstheycanutilizeinothersettingsinordertoultimatelycontributetothe developmentofnewtechnicalknowledge.

Takeleadershiprolesinaddressingdomesticorglobalbioengineeringrelatedissues. 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 theirleadershipskills,bothwithintheirteamandamongtheirotherclassmates.

CourseGrading:
40%LabReports[2total] 5%LabPerformanceandEtiquette 40%LabWriteups[2total] 10%ParticipationandGroupWorkPerformance 5%LabNotebook[completioncheckedeachsession;2formalchecksperquarter]
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CourseWeekly W Sche edule:

*Controlleddrugdeliverymodu ulemayreplaceimmobi ilizedenzym mesmodule.

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