Marcus Tindall Teaching Modelling Using Simulation Tools: Examples using Copasi and Matlab RCUK Fellow in Emerging Technologies for Systems Biology School of Biological Sciences, Department of Mathematics & Statistics, Institute for Cardiovascular and Metabolic Research and University of Reading. E-mail: [email protected].
12
Embed
Teaching Modelling Using Simulation Tools: Examples · PDF fileMarcus Tindall Teaching Modelling Using Simulation Tools: Examples using Copasi and Matlab RCUK Fellow in Emerging Technologies
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Marcus Tindall
Teaching Modelling Using
Simulation Tools: Examples
using Copasi and Matlab
RCUK Fellow in Emerging Technologies for Systems Biology
School of Biological Sciences,
Department of Mathematics & Statistics,
Institute for Cardiovascular and Metabolic Research and
• Can be used on a range of platforms – Windows, Mac, Linux.
• 3 things required to model protein reaction systems:
(i) details of the protein-protein interactions;
(ii) kinetic rate and concentration data;
(iii) more detailed understanding of mathematical
manipulation and theory including matrix
algebra, differential equations.
Matlab
• Good as the “next step up” tool for solving problems
computationally.
• Need to become familiar with the Matlab programming
language.
% Simple irreversible reaction sequence example % % A + B -> C % clear all; % Rate constants and initial concentrations k = 0.1; a0=1; b0=2; c0=0; % Solve the system of ODEs and plot the solution [t,y]=ode45(@simpreactodes, [0 50], [a0 b0 c0],'', k); plot(t,y(:,1),t,y(:,2),'r--',t,y(:,3),'g.-') xlabel('Time (seconds)'); ylabel('Concentration (mM)'); legend('a=[A]','b=[B]','c=[C]')
Matlab - Example
function simpreactodes = f(t, y, k) simpreactodes = [-k*y(1)*y(2), % a -k*y(1)*y(2) , % b k*y(1)*y(2) ]; % c
Main File Equation file
Confidence Building
• Start with a simple example students can relate to, e.g. Genetics
for Geneticists, population dynamics for Zoologists, etc..
• Make sure each part of the process is explained clearly either
beforehand or during the practical, e.g. handout, clear notes on
the web.
• Build on the initial model, e.g. Non-reversible to reversible
reactions, simple stoichometry to more complex stoichometry.
• Build in simple exercises that students can work on to gain
confidence away from the computer.
Confidence Building
• Get students thinking about the modelling process and asking
questions about what they are doing.
• Think about checking the model for “realism”, e.g. If one
reaction rate is zero and you still get the product from it, can that
be right???!!!
• Warn students about Garbage In Garbage Out (GIGO), i.e. just
believing the computer without thinking about what is going on.