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Demonstration of fitting with Berkeley Madonna

FOCUS Degradation Kinetics, Ton van der Linden, January 27, 2005. Demonstration of fitting with Berkeley Madonna. Package Version contact. Berkeley Madonna 8.0.1 www.berkeleymadonna.com. General information. Additional information.

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Demonstration of fitting with Berkeley Madonna

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

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

  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

  4. Opening screen

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

  6. Steps in the fitting procedure • Define model (equations / flow chart) • Initial values (substances / parameters) • Select parameters for fitting procedure • Set restrictions • Import datasets • Run • Export results

  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

  8. Flowchart

  9. Flowchart (simplified)

  10. Initial values • Init P = 100 • Init M1 = 0 • Init M2 = 0 • kp = .1 • km1 = .1 • km2 = .1 • fpm1=1 • fm1m2=1

  11. 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 Total user defined code

  12. {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 Code automatically defined from flowchart {

  13. Parameter selection

  14. Parameter selection Select parameters restrict Import datasets Start fitting

  15. Results

  16. graph exported as .bmp Results

  17. Results

  18. Save model / graph / table Export results

  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

  20. Results Uncertainty of parameters: Not included in package

  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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