1. FOCUS Kinetics Training: Parameter Estimation with MatLab
Dr. Dieter Schäfer
BCS / Environmental Modelling
Monheim, Germany
Presentation • March 28, 2017 • Slide 1

2. What is MatLab? MatLab ... ... stands for MATrix LABoratory
... is an interactive high-performance language for technical computing
... is a very flexible tool for solving a wide range of mathematical problems
... has a modular design (software toolboxes, ASCII control files)
... can be adapted to kinetic parameter estimation problems
=> see for further information
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

3. What is MatLab?
For the estimation of kinetic parameters, the following modules of MatLab are relevant:
MatLab (basic module) for data handling, solving of differential equations, etc.
Optimisation Toolbox for non-linear parameter optimisation
Statistics Toolbox for additional statistics
MatLab Compiler (optional) to produce stand-alone executables
current version: MatLab 7, Release 14
costs for single-user licence: € (+ Compiler 6000 €)
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

4. What is MatLab?
Potential weaknesses of MatLab in the context of FOCUS Kinetics
commercial software (costs of ~5000 € per license)
not a ready-to-use tool for kinetic parameter estimation, requires some programming skills
not too user-friendly, if run without a Graphical User Interface
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

5. What is MatLab?
Potential strengths of MatLab in the context of FOCUS Kinetics
full software support, ongoing software development
large user community in science and engineering (good availability of newsgroups, literature, experts)
extensive statistical capabilities (e.g., self-defined statistical output, including chi²-test and t-test)
extensive graphical capabilities (e.g., self-defined graphical output, development of Graphical User Interfaces)
optional generation of executable files that run independent of MatLab
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

6. On-screen Presentation of MatLab / Run via ASCII file
% KINTEST -- Test program for KINCALC
% Author: Dr. Michael Warncke, Bayer Technology Services GmbH
% Version / Date: /
% set up kinetic model
link = [1 2; 1 4; 2 3; 2 4; 3 4]; % list of connections between compartments
kinetic = {'sfo', 'sfo’, 'sfo', 'sink'}; % list of used kinetic models
% compartments
varnames = {{'P'}, {'M1'}, {'M2'}, {'S'}}; % names of state variables
boxnames = {'Parent','Met1','Met2','Sink'}; % compartment names
% kinetic parameters
paramnames = {{'kP','FFM1'}, {'kM1','ffM2'}, {'kM2'}, {}}; % names of kinetic parameters
iskfix = {[0, 0], [0, 0], [0], []}; % 0 = optimize kinetic parameters
k = {[0.05, 0.5], [0.1, 0.5], [0.01], []}; % initial values for kinetic parameters
klb = {[0, 0], [0, 0], [0], []}; % lower bounds for kinetic parameters
kub = {[Inf, Inf], [Inf, Inf], [Inf], []}; % upper bounds for kinetic parameters
% M0 values
isyfix = {[0], [1], [1], [1]}; % 0 = optimize M0
y0 = {[NaN], [0], [0], [0]}; % NaN = obtain initial M0 from data
ylb = {[0], [0], [0], [0]}; % lower bounds for M0
yub = {[Inf], [Inf], [Inf], [Inf]}; % upper bounds for M0
% assign data
model.filename = 'FOCUS-Training_Example2.txt'; % name of data file
model.datanames = {'c1','c2','c3',''}; % column names of the measurement data
model.weightnames = {'','','',''}; % column names of the weighting data
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

7. On-screen Presentation of MatLab / Run via GUI
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

8. How does MatLab perform?
Example data sets from the FOCUS Kinetics Draft Report
Data Set A (see Table 13-4a in FOCUS, 2004):
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

9. How does MatLab perform?
Example data sets from the FOCUS Kinetics Draft Report
Data Set D (see Table 13-7 in FOCUS, 2004):
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

10. How does MatLab perform?
Example data sets from the FOCUS Degradation Kinetics Training
Example 1 (parent SFO, two metabolites SFO):
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

11. How does MatLab perform?
Example data sets from the FOCUS Degradation Kinetics Training
Example 2 (parent FOMC, one metabolite SFO):
FOCUS Degradation Kinetics Training • Brussels • January 27, 2005