Boomer v2.7.7 Instructions

Red Text Lines are Instructions
Blue Characters are user entries
A) Start Boomer by double-clicking on the Boomer

               Boomer v2.7.7

      David W.A. Bourne
      OU College of Pharmacy
      1110 N.Stonewall Ave.
      Oklahoma City, OK 73117-1223
      U.S.A.                              Copyright 1986-1998 D.W.A. Bourne

      david@boomer.org

            Comput.Meth.Prog.Biomed.,29 (1989) 191-195

 Original MULTI by K. Yamaoka, et.al.

    J. Pharmacobio-Dyn., 4,879-885(1981)
    J. Pharmacobio-Dyn., 6,595-606(1983)
    J. Pharmacobio-Dyn., 8,246-256(1985)

 DATA ENTRY

  0) From KEYBOARD
  1) From .BAT file
  2) From KEYBOARD creating .BAT file
  3) From .BAT file (quiet mode)
  4) to enter data only
  5) to calculate AUC from a .DAT file

 -1) From .BAT file (with restart)
 -3) From .BAT file (quiet mode-with restart)
 -8) Shareware Registration Information
 -9) to quit

 Enter choice (0-5, -1, -3, -8 or -9) 0

 METHOD OF ANALYSIS

 0) Normal fitting
 1) Bayesian
 2) Simulation only
 3) Iterative Reweighted Least Squares
 4) Simulation with random error
 5) Grid Search

 -3) To run random number test subroutine
 -2) To close (or open) .BAT file
 -1) To finish

 Enter choice (-3 to 5) 0


 Where do you want the output?

 0) Terminal screen
 1) Disk file

 Enter choice (0-1) 0

 MODEL Definition and Parameter Entry                 * Parameter Types Allowed *

 -3) display choices    -2) display parameters   -1) to finish entry

  0) Time interrupt      1) Dose/initial amount   2) First order rate
  3) Zero order          4-5) Vm and Km of Michaelis-Menten
  6) Added constant      7) Kappa-Reciprocal volume
  8-10) C = a * EXP(-b * (X-c))
 11-13) Emax (Hill) Eq with Ec(50%) & S term     14) Second order rate
 15-17) Physiological Model Parameters (Q, V, and R)
 18) Apparent volume of distribution   19) Dummy parameter for double dependence
 20-22) C = a * SIN(2 * (X - c)/b)

 Special Functions for First-order Rate Constants

 23-24) k = a * X + b                  25-27) k = a * EXP(-b * (X - c))
 28-30) k = a * SIN(2 * (X - c)/b)
 31,32-33) dAt/dt = - k * V * Cf (Saturable Protein Binding)
 34-36) k * (1 - Imax * C/(IC(50%) + C)) Inhibition  0 or 1st order
 37-39) k * (1 + Smax * C/(SC(50%) + C)) Stimulation 0 or 1st order

 Enter type# for parameter  1 (-3 to 39) 1
 Enter parameter name Dose
 Enter Dose value 250
 0) fixed, 1) adjustable, 2) single dependence
                    or 3) double dependence 0
 Enter component to receive dose 1

 Input summary for Dose                 (type  1)

     Fixed value is    250.0    
     Dose/initial amount added to     1


 Enter 0 if happy with input, 1 if not, 2 to start over 0

 Enter type# for parameter  2 (-3 to 39) 
     enter -3 to see choices      Enter -1 to exit this section 2
 Enter parameter name kel
 Enter kel value 0.5
 0) fixed, 1) adjustable, 2) single dependence
                    or 3) double dependence 1
 Enter lower limit 0.1
 Enter upper limit 2.5
 Enter component to receive flux 0
 Enter component to lose flux 1

 Input summary for kel                  (type  2)

     Initial value   0.5000     float between   0.1000     and    2.500    
     Transfer from     1 to     0


 Enter 0 if happy with input, 1 if not, 2 to start over 0

 Enter type# for parameter  3 (-3 to 39) 
     enter -3 to see choices      Enter -1 to exit this section 18
 Enter parameter name V
 Enter V value 20
 0) fixed, 1) adjustable, 2) single dependence
                    or 3) double dependence 1
 Enter lower limit 2
 Enter upper limit 200
 Enter data set (line) number 1
 Enter line description [Cp]
 Enter component number (0 for obs x) 1

 Input summary for V                    (type 18)

     Initial value    20.00     float between    2.000     and    200.0    
     Component     1 added to line     1


 Enter 0 if happy with input, 1 if not, 2 to start over 0

 Enter type# for parameter  4 (-3 to 39) 
     enter -3 to see choices      Enter -1 to exit this section -1

 Method of Numerical Integration

 0) Classical 4th order Runge-Kutta
 1) Runge-Kutta-Gill
 2) Fehlberg RKF45
 3) Adams Predictor-Corrector with DIFSUB
 4) Gears method for stiff equations with PEDERV
 5) Gears method without PEDERV


 Enter choice (0-5) 2

 Enter Relative error term for
     Numerical integration (0.0001) 0

 Enter Absolute error term for
     Numerical integration (0.0001) 0

 FITTING METHODS

 0) Gauss-Newton
 1) Damping Gauss-Newton
 2) Marquardt
 3) Simplex
 4) Simplex->Damping GN

 Enter Choice (0-4) 4

 Enter PC for convergence (0.00001) 
 Enter description for this analysis: First Example

 Enter data from

 0) Disk file      2) ...including weights
 1) Keyboard       3) ...including weights

 Enter Choice (0-3) 1

 Enter data for [Cp]           
      Enter x-value (time) = -1 to finish data entry


 X-value (time) 1
 Y-value (concentration) 8

 X-value (time) 2
 Y-value (concentration) 5

 X-value (time) 3
 Y-value (concentration) 2.6

 X-value (time) 5
 Y-value (concentration) 0.9

 X-value (time) 6
 Y-value (concentration) 0.56

 X-value (time) -1

 Data for [Cp]           

 DATA #      Time      Concentration

      1     1.000        8.000    
      2     2.000        5.000    
      3     3.000        2.600    
      4     5.000       0.9000    
      5     6.000       0.5600    
 Do you want to

 0) Accept data
 1) Correct data point
 2) Delete data point
 3) Insert new data point
 4) Add offset to x-value

 Enter choice (0-3) 0

 Save Observed Data to Disk Module       

  Data for [Cp]           

 Select FORMAT for x-value

  0) Don't save data
  1) G14.1          2) G14.2
  3) G14.3          4) G14.4
  5) G14.5          6) G14.6
  7) F14.0          8) F14.1
  9) F14.2         10) F14.3
 11) F14.4         12) F14.5
 13) F14.6

 Enter choice (0-13) 0

 Weighting function entry for [Cp]           

 0) Equal weights
 1) Weight by 1/Cp(i)
 2) Weight by 1/Cp(i)^2
 3) Weight by 1/a*Cp(i)^b
 4) Weight by 1/(a + b*Cp(i)^c)
 5) Weight by 1/((a+b*Cp(i)^c)*d^(tn-ti))

 Data weight as a function of Cp(Obs)

 Enter choice (0-5) 2

      Time       Concentration      Weight

      1.000          8.000         0.1563E-01
      2.000          5.000         0.4000E-01
      3.000          2.600         0.1479    
      5.000         0.9000          1.235    
      6.000         0.5600          3.189    

   0.5000       20.00    
 WSS ->   0.4643E-01

   0.4859       20.42    
 WSS ->   0.9122E-01

   0.4433       20.75    
 WSS ->   0.5168    

 Progressive values of WSS

 Loop   1 - 
   1>  0.4643E-01  2>  0.9122E-01  3>  0.5168    
 Loop   2 - 
   1>  0.4643E-01  2>  0.9122E-01  3>  0.4688E-01
 Loop   3 - 
   1>  0.4643E-01  2>  0.3330E-01  3>  0.4688E-01
 Loop   4 - 
   1>  0.4643E-01  2>  0.3330E-01  3>  0.2418E-01
 Loop   5 - 
   1>  0.1814E-01  2>  0.3330E-01  3>  0.2418E-01
 Loop   6 - 
   1>  0.1814E-01  2>  0.1872E-01  3>  0.2418E-01
 Loop   7 - 
   1>  0.1814E-01  2>  0.1872E-01  3>  0.1852E-01
 Loop   8 - 
   1>  0.1814E-01  2>  0.1783E-01  3>  0.1852E-01
 Loop   9 - 
   1>  0.1814E-01  2>  0.1783E-01  3>  0.1757E-01
 Loop  10 - 
   1>  0.1716E-01  2>  0.1783E-01  3>  0.1757E-01
 Loop  11 - 
   1>  0.1716E-01  2>  0.1703E-01  3>  0.1757E-01
 Loop  12 - 
   1>  0.1716E-01  2>  0.1703E-01  3>  0.1651E-01
 Loop  13 - 
   1>  0.1652E-01  2>  0.1703E-01  3>  0.1651E-01
 Loop  14 - 
   1>  0.1652E-01  2>  0.1588E-01  3>  0.1651E-01
 Loop  15 - 
   1>  0.1562E-01  2>  0.1588E-01  3>  0.1651E-01
 Loop  16 - 
   1>  0.1562E-01  2>  0.1588E-01  3>  0.1507E-01
 Loop  17 - 
   1>  0.1562E-01  2>  0.1543E-01  3>  0.1507E-01
 Loop  18 - 
   1>  0.1441E-01  2>  0.1543E-01  3>  0.1507E-01
 Loop  19 - 
   1>  0.1441E-01  2>  0.1234E-01  3>  0.1507E-01
 Loop  20 - 
   1>  0.1441E-01  2>  0.1234E-01  3>  0.1223E-01
 Loop  21 - 
   1>  0.8715E-02  2>  0.1234E-01  3>  0.1223E-01
 Loop  22 - 
   1>  0.8715E-02  2>  0.8935E-02  3>  0.1223E-01
 Loop  23 - 
   1>  0.8715E-02  2>  0.8935E-02  3>  0.9258E-02
 Loop  24 - 
   1>  0.8715E-02  2>  0.8935E-02  3>  0.8745E-02
 Loop  25 - 
   1>  0.8715E-02  2>  0.8692E-02  3>  0.8745E-02
 Loop  26 - 
   1>  0.8715E-02  2>  0.8692E-02  3>  0.8652E-02
 Loop  27 - 
   1>  0.8642E-02  2>  0.8692E-02  3>  0.8652E-02
 Loop  28 - 
   1>  0.8642E-02  2>  0.8651E-02  3>  0.8652E-02
 Loop  29 - 
   1>  0.8642E-02  2>  0.8651E-02  3>  0.8640E-02
 Loop  30 - 
   1>  0.8642E-02  2>  0.8640E-02  3>  0.8640E-02
 Loop  31 - 
   1>  0.8637E-02  2>  0.8640E-02  3>  0.8640E-02
 Loop  32 - 
   1>  0.8637E-02  2>  0.8640E-02  3>  0.8639E-02
 Loop  33 - 
   1>  0.8637E-02  2>  0.8637E-02  3>  0.8639E-02
 Loop  34 - 
   1>  0.8637E-02  2>  0.8637E-02  3>  0.8637E-02
 Loop  35 - 
   1>  0.8637E-02  2>  0.8637E-02  3>  0.8637E-02
 Loop  36 - 
   1>  0.8637E-02  2>  0.8637E-02  3>  0.8637E-02
 Loop  37 - 
   1>  0.8637E-02  2>  0.8637E-02  3>  0.8637E-02

 ** FINAL OUTPUT FROM Boomer (v2.7.7) **      08-Mar-1999 ---  3:22:56 pm

 Title:  First Example                                               
 Input: From Keyboard
 Output:  To Computer Screen
 Data for [Cp] came from keyboard (or ?.BAT)                                             
 Fitting algorithm: Simplex Method             
 Weighting for [Cp]            by 1/Cp(Obs )^2                                      
 Numerical integration method: 2) Fehlberg RKF45                          
          with  1 de(s)
 With relative error   0.1000E-03
 With absolute error   0.1000E-03
 PC =   0.1000E-04

                    ** FINAL PARAMETER VALUES ***

  #  Name                  Value       S.D.       C.V. %  Lower <-Limit-> Upper

  1) kel                   0.54069                           0.10       2.5    
  2) V                      18.064                            2.0      0.20E+03

 AIC =   -19.7584     Final WSS =   0.863710E-02
               R-squared =   0.9998     Correlation Coeff =   0.9985    

 Initial WSS value is   0.863710E-02

 ** FINAL OUTPUT FROM Boomer (v2.7.7) **      08-Mar-1999 ---  3:22:56 pm

 Title:  First Example                                               
 Input: From Keyboard
 Output:  To Computer Screen
 Data for [Cp] came from keyboard (or ?.BAT)                                             
 Fitting algorithm: DAMPING-GAUSS/SIMPLEX      
 Weighting for [Cp]            by 1/Cp(Obs )^2                                      
 Numerical integration method: 2) Fehlberg RKF45                          
          with  1 de(s)
 With relative error   0.1000E-03
 With absolute error   0.1000E-03
 DT =   0.1000E-02     PC =   0.1000E-04 Loops =     1
 Damping =     1

                    ** FINAL PARAMETER VALUES ***

  #  Name                  Value       S.D.       C.V. %  Lower <-Limit-> Upper

  1) kel                   0.54067      0.131E-01   2.4      0.10       2.5    
  2) V                      18.064      0.916       5.1       2.0      0.20E+03

 AIC =   -19.7585     Final WSS =   0.863707E-02
               R-squared =   0.9998     Correlation Coeff =   0.9985    

 Model and Parameter Definition

  #  Name                    Value       Type From To     Dep  Start Stop

  1) Dose                =   250.0        1    0    1       0    0    0
  2) kel                 =  0.5407        2    1    0       0    0    0
  3) V                   =   18.06       18    1    1       0    0    0

 Data for [Cp]            :-

 DATA #   Time       Calculated     Observed      (Weight)   Weighted residual

     1    1.000       8.05967       8.00000      0.125000     -0.745833E-02
     2    2.000       4.69359       5.00000      0.200000      0.612826E-01
     3    3.000       2.73333       2.60000      0.384615     -0.512822E-01
     4    5.000      0.926951      0.900000       1.11111     -0.299458E-01
     5    6.000      0.539815      0.560000       1.78571      0.360454E-01

     WSS for data set  1 =   0.8637E-02
               R-squared =   0.9998     Correlation Coeff =   0.9985    

 Calculation of AUC and AUMC section

  0) Exit this section
  1) [Cp]           

 Enter line # for required AUC (0- 1) 1

 Maximum value for [Cp]            is      8.0000     at       1.000    

 Calculation of AUC and AUMC based on trapezoidal rule

 AUC and AUMC for [Cp]            using Observed data

       Time         Concentration      AUC             AUMC

      1.00000         8.00000    
     ** Note that first time point is not zero **
      2.00000         5.00000         6.50000         9.00000    
      3.00000         2.60000         10.3000         17.9000    
      5.00000        0.900000         13.8000         30.2000    
      6.00000        0.560000         14.5300         34.1300    
                                      15.5657         42.2601    

 MRT =      2.7149    

 Calculation of AUC and AUMC using Method 9 of R.D. Purves

 AUC and AUMC for [Cp]            using Observed data

       Time         Concentration      AUC             AUMC

      1.00000         8.00000    
     ** Note that first time point is not zero **
      2.00000         5.00000         6.38293         9.32531    
      3.00000         2.60000         10.0531         18.3021    
      5.00000        0.900000         13.2580         30.5654    
      6.00000        0.560000         13.9746         34.4785    
                                      15.0103         42.6086    

 MRT =      2.8386    


 Calculation of AUC and AUMC section

  0) Exit this section
  1) [Cp]           

 Enter line # for required AUC (0- 1) 0

 GRAPH OUTPUT

 0) Continue without graphical output
 1) Save data on disk for later graphing
 2) Produce a printer plot now
 3) Save for later and print now

 Enter choice (0-3) 2
Plots of observed (*) and calculated values (+)
           versus time for [Cp]           . Superimposed points (X)

    8.060      Linear                      8.060      Semi-log
 |      +                                |      +                              
 |      *                                |      *                              
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 |                                       |                  +                  
 |            *                          |                  *                  
 |            +                          |                                     
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 |                  X                    |                                     
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 |_____________________________________  |_____________________________________
   0.5398                                 0.5398    
 0              <-->             6.0     0              <-->             6.0    
 Plot of Std Wtd Residuals (X)         Plot of Std Wtd  Residuals (X)
   versus time for [Cp]                  versus calcd Cp(i) for [Cp]           

    1.142                                  1.142    
 |       X                               |                   X                 
 |                                       |                                     
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 |                                    X  |X                                    
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 0=====================================  0=====================================
 |X                                      |                                    X
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 |                            X          | X                                   
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 |              X                        |          X                          
 |                                       |                                     
  -0.9557                                -0.9557    
      1.0       <-->             6.0         0.54       <-->             8.1    

 METHOD OF ANALYSIS

 0) Normal fitting
 1) Bayesian
 2) Simulation only
 3) Iterative Reweighted Least Squares
 4) Simulation with random error
 5) Grid Search

 -3) To run random number test subroutine
 -2) To close (or open) .BAT file
 -1) To finish

 Enter choice (-3 to 5) -1