Links to other pages in this course website: HOME PAGE Canvas Site 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 485/585, Spring 2014 Computational Bioengineering NOTE: this is a draft schedule. the current schedule will be kept on the Canvas site.
	Draft Weekly Class Schedule Once the quarter has started, assignments will be uploaded to the Canvas site, not here. week Monday Lecture Wednesday Lecture Lab 1 March 31: lecture 1: Introduction to Modeling Introduction to modeling Verification 1: model building Building biochemical reaction models Post final project April 2 , lecture 2: ODE model building Model Building Tools: systems approach to linear electrical, mechanical, chemical and fluidic systems (Khoo chapter 2) Lab 1: ODE Model building optional: MATLAB Tutorial   2 April 7 , lecture 3: linear ODE solutions. (posted on canvas site) Transfer function representations Stability and steady state analysis. Verification 2: solutions April 9 , lecture 4 linear ODE systems analysis. (posted on canvas site) State space representation Bifurcation and sensitivity analysis Lab 1 due Article Discussion 1: Maitani & Verification Lab 2: Linear ODE Systems 3 <-- RETURN TO TOP April 14 , lecture 5: Nonlinear Systems Analysis Nullclines and equilibrium points Jacobian: Linearization of nonlinear systems. Validation Answer questions about final project assignment. April 16 , lecture 6 Nondimensionalization Bifurcation analysis in nonlinear systems Nondimensionalization Lab 2 due Article Discussion 2: Gardner & Validation Lab 3: Nonlinear ODE Systems Analysis 4 April 21 , lecture 7 PDE model building (transport models) gradient, divergence, laplacian, flux boundary conditions steady state solutions and characteristic times diffusion example April 23 , lecture 8 PDE solutions and analysis convection and reaction numerical solution methods Lab 3 due Discuss sample proposal (no article discussion due)   Lab 4: PDE Simulations optional: Introduction to COMSOL 5 April 28, lecture 9 Nondimensionalization for PDEs nondimensionalization Discuss project ideas April 30, lecture 10 Transport Examples Lab 4 due Article discussion 3 Project proposals due on Friday May 2 Lab 5: PDE Analysis 6 <-- RETURN TO TOP May 5, lecture 11. Stochastic Simulations Overview Review of probability distributions and statistics The MathWorld is a good reference for statistics. Discuss Project Proposals May 7 , lecture 12. Brownian Dynamics (Diffusion; Langevan Equation, Wiener Process) Lab 5 due recommended reading: Higham 2001, pp. 525–533 ONLY. Article Discussion: Nitta Lab 6 SDEs: Brownian Motion 7 May 12 , lecture 13. Stochastic chemical reaction equations Gillespie Exact, Tau-leap method, Chemical Langevin Equation recommended reading: Higham 2007 Final Project Teams Meet May 14, lecture 14 Examples of Stochastic Reaction Equations     lab 6 due Article Discussion: Artyomov   Lab 7 SDEs: Chemical Reactions 8 May 19, lecture 15. System Identification I Parameter estimation least squares measurement error and weighting schemes Milestone 1: Literature   May 21 , lecture 16. System Identification II examples Lab 7 due Lab 8 System Identification 9 <-- RETURN TO TOP May 26: MEMORIAL DAY May 28, lecture 17. Validation vs Value added in Thomas Lab Modeling Lab 8 due Milestone 2: Verification and Validation Lab 9: Milestone 3: Methods 10 June 2, Lecture 19. No Class!! milestone 4 moved to Wednesday. June 4, Review Review of course Milestone 4: Value   Lab 10 Milestone 5 course evaluations finals week Final project due: Tuesday June 10, 5 pm Oral project presentations: Wednesday, June 11, 2014,830-1020, BAG 261 enjoy the summer! <-- RETURN TO TOP
<-- RETURN TO TOP  Last Updated: June 1, 2014