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

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2 General information Package Version contact Berkeley Madonna 8.0.1 www.berkeleymadonna.com

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3 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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4 Opening screen

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5 Example Soil metabolism study, parent + two metabolites Parent Metabolite 1 Metabolite 2 Sink

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6 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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7 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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8 Flowchart

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9 Flowchart (simplified)

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10 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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11 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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12 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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13 Parameter selection

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14 Parameter selection Select parameters restrict Import datasets Start fitting

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15 Results

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16 Results graph exported as.bmp

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17 Results

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18 Export results Save model / graph / table

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19 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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20 Results Uncertainty of parameters: Not included in package

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21 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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