PBPK_public/models/humanHGplusI.json

{
   "timeUnit":"min",
   "compartments":[
      "redBloodCells","plasma","venous","kidney","urine",
      "richlyPerfused","fat","slowlyPerfused","hair",
      "brainBlood","brain",
      "liver","gut","intestine","feces",
      "plasmaI","liverI","kidneyI","hairI","brainI","fecesI"],
   "commentScaled":"add compartments that only have inputs so they can be scaled to total input",
   "scaled":["hair","hairI","feces","fecesI","urine"],
   "commentParameters":"every parameter must have a value, name is optional and used in SE computation",
   "volumeComment":"in a compartment w/o volume, value is mass",
   "volumes":{
      "plasma":"plasmaVolume",
      "venous":"venousVolume",
      "kidney":"kidneyVolume",
      "richlyPerfused":"richlyPerfusedVolume",
      "fat":"fatVolume",
      "slowlyPerfused":"slowlyPerfusedVolume",
      "brainBlood":"brainBloodVolume",
      "gut":"gutVolume",
      "intestine":"intestineVolume",
      "redBloodCells":"redBloodCellsVolume",
      "brain":"brainVolume",
      "liver":"liverVolume",
      "plasmaI":"plasmaVolume",
      "liverI":"liverVolume",
      "kidneyI":"kidneyVolume",
      "brainI":"brainVolume"
      },
   "flows":{
      "(plasma,venous):kidney":"kidneyFlow",
      "(plasma,venous):richlyPerfused":"richlyPerfusedFlow",
      "(plasma,venous):fat":"fatFlow",
      "(plasma,venous):slowlyPerfused":"slowlyPerfusedFlow",
      "(plasma,venous):brainBlood":"brainBloodFlow",
      "plasma:liver":"liverInFlow",
      "liver:venous":"liverOutFlow",
      "(plasma,liver):gut":"gutFlow",
      "plasma:venous":"plasmaFlow"},
   "commentSources":"constants in concentration units per s",
   "commentHeavyside":"value is mass of exogene/volume of container/duration",
   "inputs":{
      "intestine":"oralIngestion"},
   "commentBindings":"split to flow and diffusion dominated",
   "bindings": {
      "flowComments":"group common sources or targets with brackets",
      "flow":[
         "(kidney,richlyPerfused,fat,slowlyPerfused,brainBlood,liver)->venous",
         "gut->liver",
         "plasma->(kidney,richlyPerfused,fat,slowlyPerfused,brainBlood,liver,gut)",
         "venous->plasma"],
      "diffusion":{
         "plasma->redBloodCells":"kRBC",
         "redBloodCells->plasma":"kRBC",
         "kidney->urine":"kU",
         "slowlyPerfused->hair":"kH",
         "brainBlood->brain":"kBR",
         "brain->venous":"kBR",
         "liver->intestine":"kB",
         "intestine->gut":"kR",
         "intestine->feces":"kF",
         "plasma->liverI":"dBL",
         "liverI->plasmaI":"kLB:I",
         "liverI->fecesI":"kLF:I",
         "plasmaI->kidneyI":"kBK:I",
         "kidneyI->plasmaI":"kKB:I",
         "kidneyI->urine":"kKU:I",
         "plasmaI->hairI":"kBH:I",
         "brainI->plasmaI":"kBrB:I",
         "plasmaI->urine":"kBU:I",
         "plasmaI->brainI":"kBBr:I",
         "plasmaI->fecesI":"kBF:I",
         "plasma->brainI":"dBBr"}},
    "pcComments":"always related to outflow of organs", 
    "partitionCoefficients":{
       "kidney":"kidneyPC",
       "richlyPerfused":"richlyPerfusedPC",
       "fat":"fatPC",
       "slowlyPerfused":"slowlyPerfusedPC",
       "brainBlood":"brainBloodPC",
       "liver":"liverPC",
       "gut":"gutPC",
       "brain->venous":"brainPC",
       "redBloodCells->plasma":"rbcPC"}
}