Demonstration of fitting with Berkeley Madonna FOCUS Degradation Kinetics, Ton van der Linden, January 27, 2005.

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

Parent

Metabolite 1

Metabolite 2

Sink

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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 * Pd/dt (M1) = fpm1*kp * P - km1 * M1d/dt (M2) = fm1m2*km1 * M1 - km2 * M2

P = parentM1 = metabolite 1M2 = metabolite 2kx = degradation ratefx = 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• fpm1=1• fm1m2=1

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Total user defined code

METHOD RK4

STARTTIME = 0

STOPTIME=119

DT = 0.02

Init P = 100

Init M1 = 0

Init M2 = 0

d/dt (P) = -kp * P

d/dt (M1) = fpm1*kp * P - km1 * M1

d/dt (M2) = fm1m2*km1 * M1 - km2 * M2

kp = .1

km1 = .1

km2 = .1

fpm1=1

fm1m2=1

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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 = fPM1*kP*P

JM1M2 = fM1M2*kM1*M1

JPS = (1-fPM1)*kP*P

JM1S = (1-fM1M2)*kM1*M1

JM2S = kM2*M2

{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 parametersrestrict

Import datasetsStart fitting

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Results

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Resultsgraph exported as .bmp

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Results

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Export resultsSave 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