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Intro to modeling April 22 2011
Part of the course: Introduction to biological modeling ,[object Object],[object Object],[object Object]
Today’s goal: Learn how to solve ODE models in MATLAB
Example: Heating of water
Set the model ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Initial parameter values ,[object Object],[object Object]
Fit the experimental data with the model
P1 = 1 P2 = 1 SS = 350 P1 = 1.1 P2 = 3 SS = 55 P1 = 1.13 P2 = 4 SS = 12 Manual estimation of the parameters
How precise are the estimated parameters? ,[object Object]
Why modeling? ,[object Object],[object Object],[object Object]
Menu ,[object Object],[object Object],[object Object],[object Object],[object Object]
What’s a model?
Types of models ,[object Object],[object Object],[object Object],[object Object],[object Object],(in time) (in variable values)
How do we build a model? Grey box White box: First principles Black box: Measurements
Modeling techniques in biology ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
ODEs ,[object Object],One independent variable One or more dependent variables Order
True or false? TRUE Only valid when x is the independent variable.
Are these ODEs? YES YES Independent Dependent; Third order Independent Dependent; First order
How to solve ODEs? General Solution Particular Solution
How to solve ODEs? ,[object Object],[object Object],[object Object],[object Object]
Analytical solution Solve:
Numerical solution ,[object Object]
Taylor’s series example 1
Taylor’s series example 2
Euler’s method Under which condition is this valid?
Euler’s method Solution in multiple time-steps. Iterate: Solution in one time-step:
Example # Time steps 1 5 f(x)
What does it have to do with my ODE model? Model Initial value Step Time step
ode45 ,[object Object],[object Object],[object Object],[object Object],[object Object],Mandatory. Always put in the same order. Put it here if more info will be passed.
What do we need to use ode45? ,[object Object],[object Object],[object Object],[object Object],[object Object]
Model ,[object Object],[object Object],[object Object],[object Object]
From paper to MATLAB Identify state variables, parameters, inputs. Define equations and parameter values. Define initial values, call functions, plot results.
Example: an irreversible reaction
 
 
 
Now the language details…
20 x0 = 30 0 0 time = 0.1 0.2 … 1
Magic word: Function 0.5 p = 0.02 20 x0 = 30 0 0 time = 0.1 0.2 … 1 dxdt = 3x11 t0 t1 t2 x1 x2 x3 t3 …  t10
Summary: model function data IN OUT Row vector Row vector Matrix 20 x0 = 30 0 0 time = 0.1 0.2 … 1 dxdt = 11x3 x1 x2 x3 t0 t1 t2 t3 …  t10
0 t = 0.1 0.2 … 1 x = 11x3 x1 x2 x3 t0 t1 t2 t3 …  t10
Summary: script data IN OUT Row vector Row vector Matrix Row vector 20 x0 = 30 0 0 time = 0.1 0.2 … 1 x = 11x3 x1 x2 x3 t0 t1 t2 t3 …  t10 0 t = 0.1 0.2 … 1
From paper to MATLAB Identify state variables, parameters, inputs. Define equations and parameter values. Define initial values, call functions, plot results.
Break
A few words about programming ,[object Object],[object Object],[object Object],[object Object],[object Object]
A few words about programming ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Hands-on Tutorial
Your turn! ,[object Object]
Your turn! ,[object Object]
Homework ,[object Object]
What’s next ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 

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Intro to modelling_wur

Notes de l'éditeur

  1. Lumped parameters
  2. I’ll give an example on using experimental data.
  3. White box: Derive a model from first principles. If not possible then we have to do system identification: Black box: No prior model available. Grey box: you understand the physics of your system: you can specify an explicit mathematical model but you don’t know the parameters values
  4. An ODE describes the rate of change of a dependant variable with respect to an independent variable. The unknown element is a function. The information we have is on its derivatives.
  5. An analytical method gives the solution as a mathematical formula, which is an advantage. From this we can gain insight in the behavior and the properties of the solution, and with a numerical solution (that gives the function as a table) this is not the case
  6. Write it on the blackboard
  7. Show in blackboard how it would be if passing individual variables.
  8. Interested?