Problem number 1140744296

A First Try to Run Boomer

A drug was administered to a patient as an IV bolus dose (that is an intravenous rapid injection). Blood sample were collected at a few times after the dose was given and assayed for drug concentration. Your job is to analyse the data collected using Boomer to find the rate constant for elimination and the apparent volume of distribution.

Concentrations after an
IV Bolus Dose of 100 mg
Time (hr) Cp (mg/L)
0.5 3.24
1 3.28
2 2.68
3 2.11
6 1.07
9 0.52

Setting up Boomer

Boomer can be run on your own computer. A current versions of Boomer can be downloaded from the Boomer website. Create a new folder on your desktop or some other easily accessible place on your hard drive. Download the program from the website into this folder. If you download the file from the website you will need to decompress the program file.

There is more information (which may help - it may be out of date) as part of an earlier homework set.

Assuming you have the program on your hard drive, double-click on the program icon (Windows or earlier Macintosh) or type boomer at the prompt (Macintosh OS X). You will see something like:

 Boomer v3.3.2
                          Ref: Comput.Meth.Prog.Biomed.,29 (1989) 191-195

 David W.A. Bourne
 OU College of Pharmacy
 1110 N.Stonewall Ave.
 Oklahoma City, OK 73117-1223
 U.S.A.
                              Copyright 1986-2006 D.W.A. Bourne

 See http://www.boomer.org or email david@boomer.org for more info

 Based on the original MULTI by K. Yamaoka, et.al.
  J. Pharmacobio-Dyn., 4,879 (1981); ibid, 6,595 (1983); ibid, 8,246 (1985)

 DATA ENTRY

  0) From KEYBOARD
  1) From .BAT file                -1) From .BAT file (with restart)
  2) From KEYBOARD creating .BAT file
  3) From .BAT file (quiet mode)   -3) From .BAT file (quiet mode-with restart)
  4) to enter data only
  5) to calculate AUC from a .DAT file
 -8) Shareware Registration Information
 -9) to quit

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

Analyzing the Data

OK. Continuing on from above enter 0 to enter the information from the keyboard. Enter the text printed in red below.

 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 (0-2) 0

 MODEL Definition and Parameter Entry       * Allowed Parameter Types *

 -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 * pi * (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 * pi * (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
 40) Uniform [-1 to 1] and 41) Normal [-3 to 3] Probability
 42) Switch parameter                  43) Clone component

 Enter type# for parameter 1 (-3 to 43) 1
 Enter parameter name Dose
 Enter Dose                 value 100
 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    100.0    
     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 43) 
     enter -3 to see choices      Enter -1 to exit this section 2
 Enter parameter name Rate Constant
 Enter Rate Constant        value 0.2
 0) fixed, 1) adjustable, 2) single dependence
                    or 3) double dependence 1
 Enter lower limit 0
 Enter upper limit 5
 Enter component to receive flux 0
 Enter component to lose flux 1

 Input summary for Rate Constant        (type  2)

     Initial value    .2000     float between     .000     and    5.000    
     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 43) 
     enter -3 to see choices      Enter -1 to exit this section  18
 Enter parameter name  Apparent Volume
 Enter Apparent Volume      value 40
 0) fixed, 1) adjustable, 2) single dependence
                    or 3) double dependence 1
 Enter lower limit 1
 Enter upper limit 200
 Enter data set (line) number 1
 Enter line description [Drug]
 Enter component number (0 for obs x) 1

 Input summary for Apparent Volume      (type 18)

     Initial value    40.00     float between    1.000     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 43) 
     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) 0
 Enter description for this analysis: Homework #1 Problem Number 1140744296

 Enter data from

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

 Enter Choice (0-3) 1

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


 X-value (time) 0.5
 Y-value (concentration) 3.24

 X-value (time) 1
 Y-value (concentration) 3.28

 X-value (time) 2
 Y-value (concentration) 2.68

 X-value (time) 3
 Y-value (concentration) 2.11

 X-value (time) 6
 Y-value (concentration) 1.07

 X-value (time) 9
 Y-value (concentration) 0.52

 X-value (time) -1

 Data for [Drug]         

 DATA #      Time      Concentration

      1     0.5      3.24    
      2     1        3.28    
      3     2        2.68    
      4     3        2.11    
      5     6        1.07    
      6     9        0.52    
 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 [Drug]         

 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 [Drug]         

 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

      0.5      3.24         0.0953
      1        3.28         0.093
      2        2.68         0.1392
      3        2.11         0.2246
      6        1.07         0.8734
      9        0.52         3.6982

    .2000       40.00    
 WSS ->    4.130    

    .1676       40.69    
 WSS ->    3.922    

    .1672       34.53    
 WSS ->    3.594    

 Progressive values of WSS

 Loop   1 - 
   1>   4.130      2>   3.922      3>   3.594    
 Loop   2 - 
   1>   2.233      2>   3.922      3>   3.594    
 Loop   3 - 
   1>   2.233      2>   1.612      3>   3.594    
 Loop   4 - 
   1>   2.233      2>   1.612      3>   1.256    

........ extra stuff here

 Loop  37 - 
   1>   .4881E-01  2>   .4881E-01  3>   .4881E-01
 Loop  38 - 
   1>   .4881E-01  2>   .4881E-01  3>   .4881E-01
 Loop  39 - 
   1>   .4881E-01  2>   .4881E-01  3>   .4881E-01
 Loop  40 - 
   1>   .4881E-01  2>   .4881E-01  3>   .4881E-01

........ extra stuff here including your answers

 Calculation of AUC and AUMC section

  0) Exit this section
  1) [Drug]         

 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

 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

Before you enter the final '-1' in the next step scroll back to record the answers, i.e. Rate constant, Apparent Volume and WSS values

 Enter choice (-3 to 5) -1

 Normal Finish

Print out the ouput from this analysis using a Courier 9 point font. Note the best fit or final values for the rate constant, the apparent volume and the WSS for entry on this website.

Rate Constant
Apparent Volume
WSS


OR

Last update: Mon 26 Jun 2017 08:01:45 pm
Copyright © 2002-19 David Bourne (david@boomer.org)