Demonstration of fitting with Berkeley Madonna

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Demonstration of fitting with Berkeley Madonna

• FOCUS Degradation Kinetics, Ton van der Linden,
  January 27, 2005

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General information

• Package
• Version
• contact

• Berkeley Madonna
• 8.0.1
• www.berkeleymadonna.com

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Additional information

• Java 1.1.8 (Sun Microsystems Inc) necessary for
  using Flowchart editor
• Windows 95 or later
• Version for Macintosh available
• Free demo version available (full functionality,
  except for printing and saving)
• User guide and examples available

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Opening screen
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Example

• Soil metabolism study, parent two metabolites

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Steps in the fitting procedure

1. Define model (equations / flow chart)
2. Initial values (substances / parameters)
3. Select parameters for fitting procedure
4. Set restrictions
5. Import datasets
6. Run
7. Export results

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Define model

• d/dt (P) -kp P
• d/dt (M1) fpm1kp P - km1 M1
• d/dt (M2) fm1m2km1 M1 - km2 M2

P parent M1 metabolite 1 M2 metabolite 2 kx
degradation rate fx formation fraction
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Flowchart
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Flowchart (simplified)
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Initial values

• Init P 100
• Init M1 0
• Init M2 0
• kp .1
• km1 .1
• km2 .1
• fpm11
• fm1m21

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Total user defined code

• METHOD RK4
• STARTTIME 0
• STOPTIME119
• DT 0.02
• Init P 100
• Init M1 0
• Init M2 0

• d/dt (P) -kp P
• d/dt (M1) fpm1kp P - km1 M1
• d/dt (M2) fm1m2km1 M1 - km2 M2
• kp .1
• km1 .1
• km2 .1
• fpm11
• fm1m21

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Code automatically defined from flowchart

• Reservoirs
• d/dt (P) - JPM1 - JPS
• INIT P 100
• d/dt (M1) JPM1 - JM1M2 - JM1S
• INIT M1 0
• d/dt (M2) JM1M2 - JM2S
• INIT M2 0

• Flows
• JPM1 fPM1kPP
• JM1M2 fM1M2kM1M1
• JPS (1-fPM1)kPP
• JM1S (1-fM1M2)kM1M1
• JM2S kM2M2
• Functions
• fPM1 1
• fM1M2 1
• kP 0.1
• kM1 0.1
• kM2 0.1

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Parameter selection
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Parameter selection
Select parameters
restrict
Import datasets
Start fitting
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Results
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Results
graph exported as .bmp
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Results
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Export results
Save model / graph / table
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Results

• DT50 (parent) 13.8 d
• DT50 (metabolite 1) 6.9 d
• DT50 (metabolite 2) 60.8 d
• f.fraction (metabolite 1) 0.59
• Results are very close to results ModelMaker

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Results

• Uncertainty of parameters
• Not included in package

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Conclusions

• Berkeley Madonna
• Easy to work with
• Flexible
• Robust
• Compatible with many office packages
• Gives similar answers (results) as other packages
• Has no built-in statistical routines