Links to other pages in this course website: HOME PAGE grade book collect-it drop box Class Schedule contents: Week 1 Week 2 Week 3 Week 4 Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11	BIOEN 503, Spring 2012 Systems Bioengineering
	Class Schedule New material will be added each week, particularly as lecture notes, assignments, and solutions are added to the web site. week Wednesday Lecture Friday Lecture 1 March 28 lecture 1: Introduction to class and systems bioengineering introduction to class types of models with examples importance of verification and validation compartmental models and biochemical reactions small group excercise: build models final project posted here March 30 lecture 2: ODE model building dimensional analysis systems approach to linear electrical, mechanical, chemical and fluidic systems (Khoo chapter 2; UW restricted) hw 1 posted here! 2 April 4, lecture 3: ODE solutions and verification discussion of hw1 part 1 due steady state analysis nondimensionalization analytic solution techniques for numerical intro, see MATLAB notes on next lecture. April 6, lecture 4: computational tools for ODE solving Last names A-L start in advanced computing lab Foege N140 for MATLAB tutorial MATLAB and numerical notes. Last names M-Z start in PAA 214 for examples lecture Wilbert's tutorial ForLoop PopAnalysis PopAnalysis2 Lotka 3 <-- RETURN TO TOP April 11 , lecture 5: Linear Stability Analysis discussion of hw 1 questions 5 and 6 due. characteristic equation stable, unstable, marginally stable and oscillatory Optional linear systems extended reading   April 13 , lecture 6: Nonlinear Stability. (Supplemental - WC) nullclines and equilibrium points linearization and Jacobian eigenvalues, eigenvectors and stability example paper and stability analysis with code 4 April 18 , lecture 7: PDE model building gradient, divergence laplacian flux diffusion equation nondimensionalization convection and reaction terms converting between dimensions and coordinates For discussion (choose one paper): what does model add in the paper: Wajima ODEs Physiology , Hasty Oscillating Gene Network   April 20, lecture 8 PDE solutions (Revised to address prescribed flux boundaries) steady state solutions nondimensionalization anal & num solution methods HW 1 due 1:00 pm   5 April 25, lecture 9: PDE model solutions HW 2 posted Everyone meet in N140 computer lab!!! prepare initial analytic calculations as described in April 20th lecture! COMSOL tutorial (draft) comsol transport adsorption model (opt) comsol model documentation (opt) April 27, lecture 10: PDE examples reading discussion: Lit Paper Tissue Eng 6 <-- RETURN TO TOPwendyt May 2, lecture 11: Stochastic Models I and slides Brownian motion Langevan Equation stochastic paper biotech. Questions to discuss: how did they determine parameters? what were the advantages of using stochastic simulations? May 4, lecture 12: Stochastic Models II and slides Project description Stochastic reaction equations see software examples on my research website discussion of hw 2 Stochastic paper PNAS   7 May 9, lecture 13: System Identification typed notes from previous years system identification parameter estimation models for error local versus global minima. example sensitivity analysis code and interpretation example parameter est. code parameter estimation: screening to find the best initial guesses code to get data from published figure if you want to fit that. Homework #2 DUE (solution posted)   May 11, lecture 14: Project Discussions Discussion: project topic 1: 8 May 16, lecture 15: Proposal Overview and Background example proposal from 2011 (no preliminary data required, but otherwise close to what you need.) May 18, lecture 16: Discussion: project topic 2 : 9 <-- RETURN TO TOP May 23, lecture 17: Approach example funded grant with a hypothesis example funded grant with a device development example funded grant in R21 form May 25, lecture 18: Scientific Writing Proposals due Tuesday May 29 5:00 pm; upload to collect it and email to your peer reviewers. 10 May 30, lecture 19: Peer review instructions worksheet explained word version of worksheet June 1 , lecture 20: Peer Review Excercise Wendy will bring treats if someone reminds her this week. peer review discussions course evaluations peer review worksheets due 1:00 electronically AND in class on paper. finals week June 4, CIDR review for dept, 2:30 - 4:20 Wednesday, June 6, final proposal due 5 pm     <-- RETURN TO TOP
<-- RETURN TO TOP  Last Updated: May 30, 2012