Transcript FOCUS Kinetics Training: Parameter Estimation with MATLAB

An Introduction to the Kinetic
Evaluation Software KinGUI
Dr. Dieter Schäfer
Monheim, Germany
FOCUS Kinetics Training • Washington • January 2006
What is KinGUI ?
KinGUI ...
 ... is a kinetic evaluation software with a Graphical User
Interface
 … can handle almost all
relevant metabolic schemes
 … complies with the rules
and reporting requirements
of FOCUS Kinetics (except
water/sediment systems)
FOCUS Kinetics Training • Washington • January 2006
What is KinGUI ?
KinGUI ...
 … is based on the commercial software package MatLab
 … uses standard mathematical methods and approaches
 minimisation of the sum of squared differences
 Runge-Kutta method for numerical solution of the differential equations
 Levenberg-Marquardt algorithm for the parameter optimisation
FOCUS Kinetics Training • Washington • January 2006
What is KinGUI ?
KinGUI ...
 … was developed by BCS and an ECPA Workgroup
 … will be freely available in its executable version
 … is by no means perfect (yet), and will undergo further
testing and validation
 … is only one of several software tools for kinetic evaluations
according to FOCUS, and is used here only as an example
FOCUS Kinetics Training • Washington • January 2006
Structure of KinGUI
requires full MatLab
software package
MatLab tool
set of text files (m-files) that can be interpreted by
MatLab
Graphical User Interface
set of MatLab text files
MatLab Compiler
executable version
of KinGUI
FOCUS Kinetics Training • Washington • January 2006
requires pre-installed
MatLab environment
MatLab version
of KinGUI
How to work with KinGUI
What you need to start:
 the pre-installed MatLab environment
 the executables (kingui.exe, kingui.ctf)
 an appropriate input file
 a conceptual model of the metabolic scheme
 for a detailed introduction to KinGUI refer to the User Manual
and the Step-by-Step Guide (available as print-outs and on CD)
FOCUS Kinetics Training • Washington • January 2006
How to work with KinGUI
short presentation of KinGUI:
parent and one metabolite,
SFO kinetics
FOCUS Kinetics Training • Washington • January 2006