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

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 www.mathworks.com for further information FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

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: 4500 € (+ Compiler 6000 €) FOCUS Degradation Kinetics Training • Brussels • January 27, 2005

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

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

On-screen Presentation of MatLab / Run via ASCII file % KINTEST -- Test program for KINCALC % Author: Dr. Michael Warncke, Bayer Technology Services GmbH % Version / Date: 2.0 / 2004-12-17 % 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

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

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

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

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

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