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RE: Build a cell-cycle based tumor growth model

From: Mark Sale - Next Level Solutions <mark>
Date: Thu, 17 Jul 2008 03:50:17 -0700

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Received on Thu Jul 17 2008 - 06:50:17 EDT

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Feng,
  I don't really understand what you're trying to do , but= , it might be helpful to note that you are not required to use the compartm= ent prediction in the
Y =
statement
For example, if you have$DES
 DADT(1) = ....
 DADT(2) = ....
 DADT(3)= = ...

it is permitted to have
$ERROR
Y = A(1)/6 + LOG(A(2= )) + A(3)/S3 + EPS(1)
 

without using F (which comes from a = specific compartment).
So, you may be able to construct the data file/mo= del such that it doesn't matter which compartment the observation is assign= ed to.

In NMVI, there is a new syntax for initializing compartments<= br>
IF(A_0FLG.EQ.1) then
   A_0(2) = 1
END IF
would= this help with initializing the compartments?

WRT your second quest= ion, I can't say that I really understand, but you can set up your own comm= on as verbatim code and put whatever you want in it.
 

$DES<= br>"    FIRST
"    COMMON /MYVARS/  V= AL1, VAL2, VAL3
"    VAL1 = THETA(1)
"  &= nbsp; VAL2 = A(1)
TVAL1 = VAL1
TVAL2 = VAL2

DADT(1) = = ...
.
.
.

but, always be aware of the limits of verbatim co= de, NMTRAN does not look at it, and will not properly take the derivative o= f any expression inside.

If you're want DOUBLE PRECISION numbers, yo= u can just let NMTRAN generate the declarations for you, otherwise it gets = a little more complicated.

you can put whatever you want into it, it= will be save between calls to DES, and it available in $PK and $ERROR (you= 'll need to put in the same COMMON statements in $PK or $ERROR).

Mar= k Sale MD
Next Level Solutions, LLC
www.NextLevelSolns.com
919-846-9185

-------- Original Message --------
Subject: [NMusers] Build a cell-cycle based tumor growth model
From: Feng Yang <fyangusa Date: Thu, July 17, 2008 4:49 am
To:
D= ear nmusers:
Recently I am trying to build a cell-cycle based tumor gro= wth model, i.e. tumor size = G1+ S + G2 + M. Meanwhile, I have quite a fe= w simultaneous biomarkers to characterize the cycle behaviors.  Those = biomarkers could be calculated based on the population of G1, S, G2, and M.=   I have the following puzzles needed to be addressed:

1)&nbs= p; In my data file, what is the CMT number I should give to those observati= ons (such as tumor size and many biomarkers)?  By the way, I need CMT = to specify/initialize the corresponding compartment.   Since I am= not quite sure how to use L2 and PCMT, I tried many times, all failed exce= pt the following foolish way:
I create one more compartment to hold the= tumor size:
DADT(iTUMROR) = DADT(iG1) + DADT(iS) + DADT(iG2) + DADT(= iM)
and in my data file, I put the CMT compartment created (iTUMOR) int= o the observation of tumor size.

However, for all other biomarkers,= there is no way to write this kind of DADT equations.   How coul= d I solve this in a smart way?

2) Since some biomarker data are co= llected based on certain time point, saying t0. In other words, they are re= lative fold-changes compared to the vehicle at t0.  Therefore, I need = to save the intermediate population of G1, S, G2 and M at t0, as constants,= which will be used to scale the later-on populations so that the model pre= dictions are comparable with the observations.

However, in the bot= h block $DES and $ERROR, there is no way to save these intermediate populat= ions as global variables or constants.   I guess, I have to use M= SFO to separate the simulation to many sections?   But it am not = sure how to do it.

Your thoughts and feedback are really appreciat= ed!   Thanks a lot!

Feng

 
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