FOCUS Kinetics Training: Parameter Estimation with MatLab

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FOCUS Kinetics TrainingParameter Estimation
with MatLab

• Dr. Dieter Schäfer
• BCS / Environmental Modelling
• Monheim, Germany

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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
• gt see www.mathworks.com for further information

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What is MatLab?

• 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 )

For the estimation of kinetic parameters, the
following modules of MatLab are relevant
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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

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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

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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
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On-screen Presentation of MatLab / Run via GUI
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How does MatLab perform?

• Example data sets from the FOCUS Kinetics Draft
  Report
• Data Set A (see Table 13-4a in FOCUS, 2004)

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How does MatLab perform?

• Example data sets from the FOCUS Kinetics Draft
  Report
• Data Set D (see Table 13-7 in FOCUS, 2004)

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How does MatLab perform?

• Example data sets from the FOCUS Degradation
  Kinetics Training
• Example 1 (parent SFO, two metabolites SFO)

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How does MatLab perform?

• Example data sets from the FOCUS Degradation
  Kinetics Training
• Example 2 (parent FOMC, one metabolite SFO)