ubiquity/inst/ubinc/systems/system-mab_pk.txt at master · john-harrold/ubiquity · GitHub

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# Implementation of the two compartment model from Davda 2014
#
#   Davda, J. P., Dodds, M. G., Gibbs, M. A., Wisdom, W., & Gibbs, J. (2014). A
#   model-based meta-analysis of monoclonal antibody pharmacokinetics to guide
#   optimal first-in-human study design. mAbs, 6(4), 1094-1102.
#   http://doi.org/10.4161/mabs.29095
#
# System Units:
#   mass          [=] nmoles
#   volume        [=] L
#   concentration [=] nM
#   time          [=] day
#

# #-------------#
# | Parameters  |
# #-------------#
# System parameters
#name          value          lower  upper    units  editable grouping
#                             bound  bound
<P> F1         0.744          eps    inf      ---    yes      System
<P> ka         0.282          eps    inf      1/day  yes      System
<P> CL         0.200          eps    inf      L/day  yes      System
<P> Vc         3.61           eps    inf      L      yes      System
<P> Vp         2.75           eps    inf      L      yes      System
<P> Q          0.747          eps    inf      L/day  yes      System
<P> MW         140            eps    inf      kD     yes      System
<PSET:default>  mAb in Humans

# Interindividual Variability
# Taken from Table 3
<IIV:ETAka>    0.416
<IIV:ETAka:LN> ka

<IIV:ETACL>    0.09875
<IIV:ETACL:LN> CL

<IIV:ETAVc>    0.116
<IIV:ETAVc:LN> Vc

<IIV:ETAVp>    0.0789
<IIV:ETAVp:LN> Vp

<IIV:ETAQ>     0.699
<IIV:ETAQ:LN>  Q

<IIVCOR:ETACL:ETAVc>   0.0786
<IIVCOR:ETACL:ETAVp>   0.0619
<IIVCOR:ETAVp:ETAVc>   0.0377

# Covariates
<CV:DOSE>    ; times;      [ 0 ];    day
<CV:DOSE>    ; values;     [400];    mg
<CVINTERP:DOSE> step

<CV:WT>      ; times;      [ 0 ];    day
<CV:WT>      ; values;     [ 60];    kg
<CVINTERP:WT> step

# static secondary parameters
<As> kel = CL/Vc
<As> kcp = Q/Vc
<As> kpc = Q/Vp

# #-------------------#
# |Input Information |
# #-------------------#
#
#        1e6 ng    1 nmole             1
# X mg x ------ x ----------------- x ---  =>  X*1e3/MW/Vc
#        1 mg      MW (KDA) * 1000    V(L)
#
# Bolus Events
# times/events state   values              scale    units
<B:times>;           [  0.0, 7, 14 ];          1;   days
<B:events>;   At;    [400.0, 0, 0  ];     1e3/MW;   mg
<B:events>;   Cc;    [  0.0, 0, 0  ];  1e3/MW/Vc;   mg

<R:Dinf>;    times;     [0, 30];     1/60/24;           min
<R:Dinf>;    levels;    [0,  0];       60*24*1e3/MW;    mg/min

# ODEs
<ODE:At> -ka*At
<ODE:Cc>  ka*At*F1/Vc  -kel*Cc - kcp*Cc  + kpc*Cp*Vp/Vc + Dinf/Vc
<ODE:Cp>                                   kcp*Cc*Vc/Vp - kpc*Cp

# #---------#
# | Outputs |
# #---------#
# Outputs that begin with QC will not be displayed in the GUI

# Convert nM to ng/ml
#
#  X nM  ===> X*MW(KDA)
#
# Convert nM to ug/ml/mg(dose)
#
#  X nM  ===> X*MW(KDA)/1000/dose
#
<O> C_ng_ml = Cc*MW
<O> C_DOSE  = Cc*MW/DOSE/1000


<VP> prop_err   0.1            eps    inf      --     yes      Variance
<VP> add_err    0.1            eps    inf      ng/ml  yes      Variance

<EST:LT> Vp; Vc; CL; Q; ka
<EST:P>  Vp; Vc; CL; Q; ka; add_err; prop_err
<OE:C_ng_ml> add=add_err; prop=prop_err
<AMTIFY> Cp; Ap; Vp

# #---------#
# | Options #
# #---------#
# General Options:
# specify different time scales
<TS:min>   24.0*60.0
<TS:days>  1.0
<TS:hours> 24.0
<TS:weeks> 1.0/7.0
<TS:months> 1.0/7.0/4.0