RE: [NMusers] Build a cell-cycle based tumor growth model

[Mark Sale - Next Level Solutions]

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 compartment 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/model such that it doesn't matter which compartment the observation is assigned to. In NMVI, there is a new syntax for initializing compartments IF(A_0FLG.EQ.1) then    A_0(2) = 1 END IF would this help with initializing the compartments? WRT your second question, I can't say that I really understand, but you can set up your own common as verbatim code and put whatever you want in it.   $DES "    FIRST "    COMMON /MYVARS/  VAL1, VAL2, VAL3 "    VAL1 = THETA(1) "    VAL2 = A(1) TVAL1 = VAL1 TVAL2 = VAL2 DADT(1) = ... . . . but, always be aware of the limits of verbatim code, NMTRAN does not look at it, and will not properly take the derivative of any _expression_ inside. If you're want DOUBLE PRECISION numbers, you 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). Mark 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" <[EMAIL PROTECTED]> Date: Thu, July 17, 2008 4:49 am To: nmusers@globomaxnm.com Dear nmusers: Recently I am trying to build a cell-cycle based tumor growth model, i.e. tumor size = G1+ S + G2 + M. Meanwhile, I have quite a few 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)  In my data file, what is the CMT number I should give to those observations (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 except 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) into the observation of tumor size. However, for all other biomarkers, there is no way to write this kind of DADT equations.   How could I solve this in a smart way? 2) Since some biomarker data are collected based on certain time point, saying t0. In other words, they are relative 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 predictions are comparable with the observations. However, in the both block $DES and $ERROR, there is no way to save these intermediate populations as global variables or constants.   I guess, I have to use MSFO to separate the simulation to many sections?   But it am not sure how to do it. Your thoughts and feedback are really appreciated!   Thanks a lot! Feng