Transcript Demonstration of fitting with Berkeley Madonna

FOCUS Degradation Kinetics, Ton van der Linden, January 27, 2005
Demonstration of fitting with
Berkeley Madonna
General information
Package
Berkeley Madonna
Version
8.0.1
contact
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
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Define model (equations / flow chart)
Initial values (substances / parameters)
Select parameters for fitting procedure
Set restrictions
Import datasets
Run
Export results
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Define model
d/dt (P) = -kp * P
d/dt (M1) = fpm1*kp * P - km1 * M1
d/dt (M2) = fm1m2*km1 * 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
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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
d/dt (P) = -kp * P
d/dt (M1) = fpm1*kp * P - km1 * M1
STARTTIME = 0
d/dt (M2) = fm1m2*km1 * M1 - km2 * M2
STOPTIME=119
DT = 0.02
kp = .1
km1 = .1
Init P = 100
km2 = .1
Init M1 = 0
fpm1=1
Init M2 = 0
fm1m2=1
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Code automatically defined from flowchart
{Reservoirs}
{Flows}
d/dt (P) = - JPM1 - JPS
JPM1 = fPM1*kP*P
INIT P = 100
JM1M2 = fM1M2*kM1*M1
d/dt (M1) = + JPM1 - JM1M2 - JM1S
INIT M1 = 0
JPS = (1-fPM1)*kP*P
JM1S = (1-fM1M2)*kM1*M1
d/dt (M2) = + JM1M2 - JM2S
JM2S = kM2*M2
INIT M2 = 0
{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
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