Adding models where PC:plasma is adjusted for RBC content

models/humanHG_RBC.json

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+{
+   "timeUnit":"min",
+   "compartments":[
+      "redBloodCells","plasma","venous","kidney","urine",
+      "richlyPerfused","fat","slowlyPerfused","hair",
+      "brainBlood","brain",
+      "liver","gut","intestine","feces","inorganicMercury"],
+   "commentScaled":"add compartments that only have inputs so they can be scaled to total input",
+   "scaled":["hair","inorganicMercury","feces","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"
+      },
+   "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",
+         "liver->inorganicMercury":"kI",
+         "intestine->gut":"kR",
+         "intestine->inorganicMercury":"kD",
+         "intestine->feces":"kF",
+         "inorganicMercury->feces":"kIF"}},
+    "pcComments":"always related to outflow of organs", 
+    "partitionCoefficients":{
+       "kidney":"kidneyPCplasma",
+       "richlyPerfused":"richlyPerfusedPCplasma",
+       "fat":"fatPCplasma",
+       "slowlyPerfused":"slowlyPerfusedPCplasma",
+       "brainBlood":"brainBloodPCplasma",
+       "liver":"liverPCplasma",
+       "gut":"gutPCplasma",
+       "brain->venous":"brainPCplasma",
+       "redBloodCells->plasma":"rbcPCplasma"}
+}

models/humanHG_RBC_parameters.json

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+{"parameters":{
+    "bodyWeight":{"value":67.77,"units":"kg","dist":"lognormal","cv":0.26},
+    "bwPower0p75":{"derived":"bwPower0p75"},
+    "commentInputs":"X",
+    "oralIngestion":{"value":0.0486,"unit":"ug/min","dist":"normal","cv":0.1},
+    "commentPC":"X",
+    "bloodToPlasmaPCscale":{"derived":"bloodToPlasmaPCscale"},
+    "rbcPCfraction":{"derived":"rbcPCfraction"},
+    "brainBloodPCplasma":{"value":1,"dist":"lognormal","cv":0.3},
+    "brainPCblood":{"value":3,"dist":"lognormal","cv":0.3},
+    "fatPCblood":{"value":0.15,"dist":"lognormal","cv":0.3},
+    "gutPCblood":{"value":1,"dist":"lognormal","cv":0.7},
+    "kidneyPCblood":{"value":4.0,"dist":"lognormal","cv":0.3},
+    "liverPCblood":{"value":5.0,"dist":"lognormal","cv":0.3},
+    "rbcPCplasma":{"value":12.0,"dist":"lognormal","cv":0.3},
+    "richlyPerfusedPCblood":{"value":1.0,"dist":"lognormal","cv":0.3},
+    "slowlyPerfusedPCblood":{"value":2.0,"dist":"lognormal","cv":0.3},
+    "commentPCplasma":"X",
+    "brainPCplasma":{"derived":"brainPCplasma"},
+    "fatPCplasma":{"derived":"fatPCplasma"},
+    "gutPCplasma":{"derived":"gutPCplasma"},
+    "kidneyPCplasma":{"derived":"kidneyPCplasma"},
+    "liverPCplasma":{"derived":"liverPCplasma"},
+    "richlyPerfusedPCplasma":{"derived":"richlyPerfusedPCplasma"},
+    "slowlyPerfusedPCplasma":{"derived":"slowlyPerfusedPCplasma"},
+    "commentCardiacOutput":"X",
+    "cardiacOutput":{"derived":"cardiacOutput"},
+    "cardiacOutputScaled":{"value":0.333,"unit":"l/min","dist":"normal","cv":0.22},
+    "commentFlows":"X",
+    "plasmaFlow":{"derived":"plasmaFlow"},
+    "kidneyFlow":{"derived":"kidneyFlow"},
+    "richlyPerfusedFlow":{"derived":"richlyPerfusedFlow"},
+    "fatFlow":{"derived":"fatFlow"},
+    "slowlyPerfusedFlow":{"derived":"slowlyPerfusedFlow"},
+    "brainBloodFlow":{"derived":"brainBloodFlow"},
+    "liverInFlow":{"derived":"liverInFlow"},
+    "liverOutFlow":{"derived":"liverOutFlow"},
+    "gutFlow":{"derived":"gutFlow"},
+    "commentFlowFraction":"X",
+    "plasmaFlowFraction":{"value":1},
+    "kidneyFlowFraction":{"value":0.175,"dist":"normal","cv":0.3},
+    "richlyPerfusedFlowFraction":{"value":0.183,"dist":"normal","cv":0.3},
+    "fatFlowFraction":{"value":0.052,"dist":"normal","cv":0.3},
+    "slowlyPerfusedFlowFraction":{"value":0.249,"dist":"normal","cv":0.3},
+    "brainBloodFlowFraction":{"value":0.114,"dist":"normal","cv":0.3},
+    "liverInFlowFraction":{"value":0.046,"dist":"normal","cv":0.32},
+    "commentLiverOutFlow":"sum of liver in and gut",
+    "liverOutFlowFraction":{"value":0.227,"dist":"normal","cv":0.3},
+    "gutFlowFraction":{"value":0.181,"dist":"normal","cv":0.33},
+    "commentVolumes":"X",
+    "plasmaVolume":{"derived":"plasmaVolume"},
+    "venousVolume":{"derived":"venousVolume"},
+    "redBloodCellsVolume":{"derived":"redBloodCellsVolume"},
+    "kidneyVolume":{"derived":"kidneyVolume"},
+    "richlyPerfusedVolume":{"derived":"richlyPerfusedVolume"},
+    "fatVolume":{"derived":"fatVolume"},
+    "slowlyPerfusedVolume":{"derived":"slowlyPerfusedVolume"},
+    "brainBloodVolume":{"derived":"brainBloodVolume"},
+    "brainVolume":{"derived":"brainVolume"},
+    "liverVolume":{"derived":"liverVolume"},
+    "gutVolume":{"derived":"gutVolume"},
+    "intestineVolume":{"derived":"intestineVolume"},
+    "commentFractionsDerived":"X",
+    "plasmaVolumeFractionBlood":{"derived":"plasmaVolumeFractionBlood"},
+    "rbcVolumeFractionBlood":{"derived":"rbcVolumeFractionBlood"},
+    "bloodVolumeFraction":{"derived":"bloodVolumeFraction"},
+    "venousVolumeFraction":{"derived":"venousVolumeFraction"},
+    "plasmaVolumeFraction":{"derived":"plasmaVolumeFraction"},
+    "commentFractions":"X",
+    "plasmaTotalVolumeFraction":{"value":0.04,"dist":"normal","cv":0.14},
+    "redBloodCellsVolumeFraction":{"value":0.024,"dist":"normal","cv":0.25},
+    "kidneyVolumeFraction":{"value":0.004,"dist":"normal","cv":0.3},
+    "richlyPerfusedVolumeFraction":{"value":0.1,"dist":"normal","cv":0.3},
+    "fatVolumeFraction":{"value":0.273,"dist":"normal","cv":0.24},
+    "hairVolumeFraction":{"value":0.002,"dist":"normal","cv":0.5},
+    "slowlyPerfusedVolumeFraction":{"value":0.35,"dist":"normal","cv":0.16},
+    "brainBloodVolumeFraction":{"value":0.007,"dist":"normal","cv":0.3},
+    "brainVolumeFraction":{"value":0.02,"dist":"normal","cv":0.3},
+    "liverVolumeFraction":{"value":0.026,"dist":"normal","cv":0.25},
+    "gutVolumeFraction":{"value":0.017,"dist":"normal","cv":0.15},
+    "intestineVolumeFraction":{"value":0.014,"dist":"normal","cv":0.3},
+    "commentDiff":"X",
+    "kB":{"derived":"kB"},
+    "kBR":{"derived":"kBR"},
+    "kD":{"derived":"kD"},
+    "kF":{"derived":"kF"},
+    "kH":{"derived":"kH"},
+    "kI":{"derived":"kI"},
+    "kIF":{"derived":"kIF"},
+    "kRBC":{"derived":"kRBC"},
+    "kR":{"derived":"kR"},
+    "kU":{"derived":"kU"},
+    "commentDiffScaled":"X",
+    "kBScaled":{"value":1.67e-6,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kBRScaled":{"value":1.67e-4,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kDScaled":{"value":1e-4,"unit":"l/hour","dist":"lognormal","cv":0.3},
+    "kFScaled":{"value":2e-4,"unit":"l/hour","dist":"lognormal","cv":0.36},
+    "kHScaled":{"value":7e-6,"unit":"l/hour","dist":"lognormal","cv":0.25},
+    "kIScaled":{"value":1e-5,"unit":"l/hour","dist":"lognormal","cv":0.3},
+    "kIFScaled":{"value":0,"unit":"l/min","noDist":"lognormal","cv":0.3},
+    "kRBCScaled":{"value":2.5e-2,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kRScaled":{"value":8.33e-5,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kUScaled":{"value":0,"unit":"l/min"},
+    "zero":{"value":0},
+    "threeQuarters":{"value":0.75}},
+"derivedParameters":{
+    "bwPower0p75":{
+        "type":"power",
+        "a":"bodyWeight",
+        "n":"threeQuarters"},
+    "cardiacOutput":{
+        "type":"product",
+        "a":"cardiacOutputScaled",
+        "b":"bwPower0p75"},
+    "plasmaFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"plasmaFlowFraction"},
+    "kidneyFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"kidneyFlowFraction"},
+    "richlyPerfusedFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"richlyPerfusedFlowFraction"},
+    "fatFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"fatFlowFraction"},
+    "slowlyPerfusedFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"slowlyPerfusedFlowFraction"},
+    "brainBloodFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"brainBloodFlowFraction"},
+    "liverInFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"liverInFlowFraction"},
+    "liverOutFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"liverOutFlowFraction"},
+    "gutFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"gutFlowFraction"},
+    "bloodToPlasmaPCscale":{
+        "type":"sum",
+        "a":"plasmaVolumeFractionBlood",
+        "b":"rbcPCfraction"},
+    "rbcPCfraction":{
+        "type":"product",
+        "a":"rbcVolumeFractionBlood",
+        "b":"rbcPCplasma"},
+    "brainPCplasma":{
+        "type":"product",
+        "a":"brainPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "kidneyPCplasma":{
+        "type":"product",
+        "a":"kidneyPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "richlyPerfusedPCplasma":{
+        "type":"product",
+        "a":"richlyPerfusedPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "slowlyPerfusedPCplasma":{
+        "type":"product",
+        "a":"slowlyPerfusedPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "fatPCplasma":{
+        "type":"product",
+        "a":"fatPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "gutPCplasma":{
+        "type":"product",
+        "a":"gutPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "liverPCplasma":{
+        "type":"product",
+        "a":"liverPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "plasmaVolume":{
+        "type":"product",
+        "a":"plasmaVolumeFraction",
+        "b":"bodyWeight"},
+    "venousVolume":{
+        "type":"product",
+        "a":"venousVolumeFraction",
+        "b":"bodyWeight"},
+    "redBloodCellsVolume":{
+        "type":"product",
+        "a":"redBloodCellsVolumeFraction",
+        "b":"bodyWeight"},
+    "kidneyVolume":{
+        "type":"product",
+        "a":"kidneyVolumeFraction",
+        "b":"bodyWeight"},
+    "richlyPerfusedVolume":{
+        "type":"product",
+        "a":"richlyPerfusedVolumeFraction",
+        "b":"bodyWeight"},
+    "fatVolume":{
+        "type":"product",
+        "a":"fatVolumeFraction",
+        "b":"bodyWeight"},
+    "slowlyPerfusedVolume":{
+        "type":"product",
+        "a":"slowlyPerfusedVolumeFraction",
+        "b":"bodyWeight"},
+    "brainBloodVolume":{
+        "type":"product",
+        "a":"brainBloodVolumeFraction",
+        "b":"bodyWeight"},
+    "brainVolume":{
+        "type":"product",
+        "a":"brainVolumeFraction",
+        "b":"bodyWeight"},
+    "liverVolume":{
+        "type":"product",
+        "a":"liverVolumeFraction",
+        "b":"bodyWeight"},
+    "gutVolume":{
+        "type":"product",
+        "a":"gutVolumeFraction",
+        "b":"bodyWeight"},
+    "intestineVolume":{
+        "type":"product",
+        "a":"intestineVolumeFraction",
+        "b":"bodyWeight"},
+    "plasmaVolumeFractionBlood":{
+        "type":"ratio",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"bloodVolumeFraction"},
+    "rbcVolumeFractionBlood":{
+        "type":"ratio",
+        "a":"redBloodCellsVolumeFraction",
+        "b":"bloodVolumeFraction"},
+    "plasmaVolumeFraction":{
+        "type":"ratio",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"two"},
+    "venousVolumeFraction":{
+        "type":"ratio",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"two"},
+    "bloodVolumeFraction":{
+        "type":"sum",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"redBloodCellsVolumeFraction"},
+    "kB":{
+        "type":"product",
+        "a":"kBScaled",
+        "b":"bwPower0p75"},
+    "kBR":{
+        "type":"product",
+        "a":"kBRScaled",
+        "b":"bwPower0p75"},
+    "kD":{
+        "type":"product",
+        "a":"kDScaled",
+        "b":"bwPower0p75"},
+    "kF":{
+        "type":"product",
+        "a":"kFScaled",
+        "b":"bwPower0p75"},
+    "kH":{
+        "type":"product",
+        "a":"kHScaled",
+        "b":"bwPower0p75"},
+    "kI":{
+        "type":"product",
+        "a":"kIScaled",
+        "b":"bwPower0p75"},
+    "kIF":{
+        "type":"product",
+        "a":"kIFScaled",
+        "b":"bwPower0p75"},
+    "kRBC":{
+        "type":"product",
+        "a":"kRBCScaled",
+        "b":"bwPower0p75"},
+    "kR":{
+        "type":"product",
+        "a":"kRScaled",
+        "b":"bwPower0p75"},
+    "kU":{
+        "type":"product",
+        "a":"kUScaled",
+        "b":"bwPower0p75"}}
+}

models/humanHGplusI_RBC.json

@@ -0,0 +1,86 @@
+{
+   "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":"kidneyPCplasma",
+        "richlyPerfused":"richlyPerfusedPCplasma",
+        "fat":"fatPCplasma",
+        "slowlyPerfused":"slowlyPerfusedPCplasma",
+        "brainBlood":"brainBloodPCplasma",
+        "liver":"liverPCplasma",
+        "gut":"gutPCplasma",
+        "brain->venous":"brainPCplasma",
+        "redBloodCells->plasma":"rbcPCplasma"}
+}

models/humanHGplusI_RBC_parameters.json

@@ -0,0 +1,369 @@
+{"parameters":{
+    "bodyWeight":{"value":67.77,"units":"kg","dist":"lognormal","cv":0.26},
+    "bwPower0p75":{"derived":"bwPower0p75"},
+    "commentInputs":"X",
+    "oralIngestion":{"value":0.0486,"unit":"ug/min"},
+    "commentPC":"X",
+    "bloodToPlasmaPCscale":{"derived":"bloodToPlasmaPCscale"},
+    "rbcPCfraction":{"derived":"rbcPCfraction"},
+    "brainBloodPCplasma":{"value":1,"dist":"lognormal","cv":0.3},
+    "brainPCblood":{"value":3,"dist":"lognormal","cv":0.3},
+    "fatPCblood":{"value":0.15,"dist":"lognormal","cv":0.3},
+    "gutPCblood":{"value":1,"dist":"lognormal","cv":0.7},
+    "kidneyPCblood":{"value":4.0,"dist":"lognormal","cv":0.3},
+    "liverPCblood":{"value":5.0,"dist":"lognormal","cv":0.3},
+    "rbcPCplasma":{"value":12.0,"dist":"lognormal","cv":0.3},
+    "richlyPerfusedPCblood":{"value":1.0,"dist":"lognormal","cv":0.3},
+    "slowlyPerfusedPCblood":{"value":2.0,"dist":"lognormal","cv":0.3},
+    "commentPCplasma":"X",
+    "brainPCplasma":{"derived":"brainPCplasma"},
+    "fatPCplasma":{"derived":"fatPCplasma"},
+    "gutPCplasma":{"derived":"gutPCplasma"},
+    "kidneyPCplasma":{"derived":"kidneyPCplasma"},
+    "liverPCplasma":{"derived":"liverPCplasma"},
+    "richlyPerfusedPCplasma":{"derived":"richlyPerfusedPCplasma"},
+    "slowlyPerfusedPCplasma":{"derived":"slowlyPerfusedPCplasma"},
+    "commentCardiacOutput":"X",
+    "cardiacOutput":{"derived":"cardiacOutput"},
+    "cardiacOutputScaled":{"value":0.333,"unit":"l/min","dist":"normal","cv":0.22},
+    "commentFlows":"X",
+    "plasmaFlow":{"derived":"plasmaFlow"},
+    "kidneyFlow":{"derived":"kidneyFlow"},
+    "richlyPerfusedFlow":{"derived":"richlyPerfusedFlow"},
+    "fatFlow":{"derived":"fatFlow"},
+    "slowlyPerfusedFlow":{"derived":"slowlyPerfusedFlow"},
+    "brainBloodFlow":{"derived":"brainBloodFlow"},
+    "liverInFlow":{"derived":"liverInFlow"},
+    "liverOutFlow":{"derived":"liverOutFlow"},
+    "gutFlow":{"derived":"gutFlow"},
+    "commentFlowFraction":"X",
+    "plasmaFlowFraction":{"value":1},
+    "kidneyFlowFraction":{"value":0.175,"dist":"normal","cv":0.3},
+    "richlyPerfusedFlowFraction":{"value":0.183,"dist":"normal","cv":0.3},
+    "fatFlowFraction":{"value":0.052,"dist":"normal","cv":0.3},
+    "slowlyPerfusedFlowFraction":{"value":0.249,"dist":"normal","cv":0.3},
+    "brainBloodFlowFraction":{"value":0.114,"dist":"normal","cv":0.3},
+    "liverInFlowFraction":{"value":0.046,"dist":"normal","cv":0.32},
+    "commentLiverOutFlow":"sum of liver in and gut",
+    "liverOutFlowFraction":{"value":0.227,"dist":"normal","cv":0.3},
+    "gutFlowFraction":{"value":0.181,"dist":"normal","cv":0.33},
+    "commentVolumes":"X",
+    "plasmaVolume":{"derived":"plasmaVolume"},
+    "venousVolume":{"derived":"venousVolume"},
+    "redBloodCellsVolume":{"derived":"redBloodCellsVolume"},
+    "kidneyVolume":{"derived":"kidneyVolume"},
+    "richlyPerfusedVolume":{"derived":"richlyPerfusedVolume"},
+    "fatVolume":{"derived":"fatVolume"},
+    "slowlyPerfusedVolume":{"derived":"slowlyPerfusedVolume"},
+    "brainBloodVolume":{"derived":"brainBloodVolume"},
+    "brainVolume":{"derived":"brainVolume"},
+    "liverVolume":{"derived":"liverVolume"},
+    "gutVolume":{"derived":"gutVolume"},
+    "intestineVolume":{"derived":"intestineVolume"},
+    "commentFractionsDerived":"X",
+    "plasmaVolumeFractionBlood":{"derived":"plasmaVolumeFractionBlood"},
+    "rbcVolumeFractionBlood":{"derived":"rbcVolumeFractionBlood"},
+    "bloodVolumeFraction":{"derived":"bloodVolumeFraction"},
+    "venousVolumeFraction":{"derived":"venousVolumeFraction"},
+    "plasmaVolumeFraction":{"derived":"plasmaVolumeFraction"},
+    "commentFractions":"X",
+    "plasmaTotalVolumeFraction":{"value":0.04,"dist":"normal","cv":0.14},
+    "redBloodCellsVolumeFraction":{"value":0.024,"dist":"normal","cv":0.25},
+    "kidneyVolumeFraction":{"value":0.004,"dist":"normal","cv":0.3},
+    "richlyPerfusedVolumeFraction":{"value":0.1,"dist":"normal","cv":0.3},
+    "fatVolumeFraction":{"value":0.273,"dist":"normal","cv":0.24},
+    "hairVolumeFraction":{"value":0.002,"dist":"normal","cv":0.5},
+    "slowlyPerfusedVolumeFraction":{"value":0.35,"dist":"normal","cv":0.16},
+    "brainBloodVolumeFraction":{"value":0.007,"dist":"normal","cv":0.3},
+    "brainVolumeFraction":{"value":0.02,"dist":"normal","cv":0.3},
+    "liverVolumeFraction":{"value":0.026,"dist":"normal","cv":0.25},
+    "gutVolumeFraction":{"value":0.017,"dist":"normal","cv":0.15},
+    "intestineVolumeFraction":{"value":0.014,"dist":"normal","cv":0.3},
+    "commentDiff":"X",
+    "kB":{"derived":"kB"},
+    "kBR":{"derived":"kBR"},
+    "kD":{"derived":"kD"},
+    "kF":{"derived":"kF"},
+    "kH":{"derived":"kH"},
+    "kI":{"derived":"kI"},
+    "kIF":{"derived":"kIF"},
+    "kRBC":{"derived":"kRBC"},
+    "kR":{"derived":"kR"},
+    "kU":{"derived":"kU"},
+    "commentInorganicMercury":"X",
+    "dBL":{"derived":"dBL"},
+    "dBBr":{"derived":"dBBr"},
+    "kLB:I":{"derived":"kLB:I"},
+    "kBK:I":{"derived":"kBK:I"},
+    "kKB:I":{"derived":"kKB:I"},
+    "kKU:I":{"derived":"kKU:I"},
+    "kBH:I":{"derived":"kBH:I"},
+    "kBU:I":{"derived":"kBU:I"},
+    "kBF:I":{"derived":"kBF:I"},
+    "kLF:I":{"derived":"kLF:I"},
+    "kBBr:I":{"derived":"kBBr:I"},
+    "kBrB:I":{"derived":"kBrB:I"},
+    "commentDiffScaled":"X",
+    "kBScaled":{"value":1.67e-6,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kBRScaled":{"value":1.67e-4,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kDScaled":{"value":1e-4,"unit":"l/hour","dist":"lognormal","cv":0.3},
+    "kFScaled":{"value":2e-4,"unit":"l/hour","dist":"lognormal","cv":0.36},
+    "kHScaled":{"value":7e-6,"unit":"l/hour","dist":"lognormal","cv":0.25},
+    "kIScaled":{"value":1e-5,"unit":"l/hour","dist":"lognormal","cv":0.3},
+    "kIFScaled":{"value":0,"unit":"l/min","noDist":"lognormal","cv":0.3},
+    "kRBCScaled":{"value":2.5e-2,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kRScaled":{"value":8.33e-5,"unit":"l/min","dist":"lognormal","cv":0.3},
+    "kUScaled":{"value":0,"unit":"l/min"},
+    "commentInorganicMerucryFromPaper":"X",
+    "dBLPaper":{"value":0.175,"unit":"/day","dist":"lognormal","cv":0.3},
+    "dBBrPaper":{"value":0.0,"unit":"/day","noDist":"lognormal","cv":0.3},
+    "kLB:IPaper":{"value":0.894,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kBK:IPaper":{"value":17.1234,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kKB:IPaper":{"value":0.001,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kKU:IPaper":{"value":0.006949,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kBH:IPaper":{"value":0.14,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kBU:IPaper":{"value":0.006949,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kBF:IPaper":{"value":3.9917,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kLF:IPaper":{"value":1.5476,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kBBr:IPaper":{"value":0.0028,"unit":"/day","dist":"lognormal","cv":0.3},
+    "kBrB:IPaper":{"value":0.052,"unit":"/day","dist":"lognormal","cv":0.3},
+    "zero":{"value":0},
+    "threeQuarters":{"value":0.75}},
+"derivedParameters":{
+    "bwPower0p75":{
+        "type":"power",
+        "a":"bodyWeight",
+        "n":"threeQuarters"},
+    "cardiacOutput":{
+        "type":"product",
+        "a":"cardiacOutputScaled",
+        "b":"bwPower0p75"},
+    "plasmaFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"plasmaFlowFraction"},
+    "kidneyFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"kidneyFlowFraction"},
+    "richlyPerfusedFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"richlyPerfusedFlowFraction"},
+    "fatFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"fatFlowFraction"},
+    "slowlyPerfusedFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"slowlyPerfusedFlowFraction"},
+    "brainBloodFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"brainBloodFlowFraction"},
+    "liverInFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"liverInFlowFraction"},
+    "liverOutFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"liverOutFlowFraction"},
+    "gutFlow":{
+        "type":"product",
+        "a":"cardiacOutput",
+        "b":"gutFlowFraction"},
+    "bloodToPlasmaPCscale":{
+        "type":"sum",
+        "a":"plasmaVolumeFractionBlood",
+        "b":"rbcPCfraction"},
+    "rbcPCfraction":{
+        "type":"product",
+        "a":"rbcVolumeFractionBlood",
+        "b":"rbcPCplasma"},
+    "brainPCplasma":{
+        "type":"product",
+        "a":"brainPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "kidneyPCplasma":{
+        "type":"product",
+        "a":"kidneyPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "richlyPerfusedPCplasma":{
+        "type":"product",
+        "a":"richlyPerfusedPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "slowlyPerfusedPCplasma":{
+        "type":"product",
+        "a":"slowlyPerfusedPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "fatPCplasma":{
+        "type":"product",
+        "a":"fatPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "gutPCplasma":{
+        "type":"product",
+        "a":"gutPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "liverPCplasma":{
+        "type":"product",
+        "a":"liverPCblood",
+        "b":"bloodToPlasmaPCscale"},
+    "plasmaVolume":{
+        "type":"product",
+        "a":"plasmaVolumeFraction",
+        "b":"bodyWeight"},
+    "venousVolume":{
+        "type":"product",
+        "a":"venousVolumeFraction",
+        "b":"bodyWeight"},
+    "redBloodCellsVolume":{
+        "type":"product",
+        "a":"redBloodCellsVolumeFraction",
+        "b":"bodyWeight"},
+    "kidneyVolume":{
+        "type":"product",
+        "a":"kidneyVolumeFraction",
+        "b":"bodyWeight"},
+    "richlyPerfusedVolume":{
+        "type":"product",
+        "a":"richlyPerfusedVolumeFraction",
+        "b":"bodyWeight"},
+    "fatVolume":{
+        "type":"product",
+        "a":"fatVolumeFraction",
+        "b":"bodyWeight"},
+    "slowlyPerfusedVolume":{
+        "type":"product",
+        "a":"slowlyPerfusedVolumeFraction",
+        "b":"bodyWeight"},
+    "brainBloodVolume":{
+        "type":"product",
+        "a":"brainBloodVolumeFraction",
+        "b":"bodyWeight"},
+    "brainVolume":{
+        "type":"product",
+        "a":"brainVolumeFraction",
+        "b":"bodyWeight"},
+    "liverVolume":{
+        "type":"product",
+        "a":"liverVolumeFraction",
+        "b":"bodyWeight"},
+    "gutVolume":{
+        "type":"product",
+        "a":"gutVolumeFraction",
+        "b":"bodyWeight"},
+    "intestineVolume":{
+        "type":"product",
+        "a":"intestineVolumeFraction",
+        "b":"bodyWeight"},
+    "plasmaVolumeFractionBlood":{
+        "type":"ratio",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"bloodVolumeFraction"},
+    "rbcVolumeFractionBlood":{
+        "type":"ratio",
+        "a":"redBloodCellsVolumeFraction",
+        "b":"bloodVolumeFraction"},
+    "plasmaVolumeFraction":{
+        "type":"ratio",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"two"},
+    "venousVolumeFraction":{
+        "type":"ratio",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"two"},
+    "bloodVolumeFraction":{
+        "type":"sum",
+        "a":"plasmaTotalVolumeFraction",
+        "b":"redBloodCellsVolumeFraction"},    
+    "kB":{
+        "type":"product",
+        "a":"kBScaled",
+        "b":"bwPower0p75"},
+    "kBR":{
+        "type":"product",
+        "a":"kBRScaled",
+        "b":"bwPower0p75"},
+    "kD":{
+        "type":"product",
+        "a":"kDScaled",
+        "b":"bwPower0p75"},
+    "kF":{
+        "type":"product",
+        "a":"kFScaled",
+        "b":"bwPower0p75"},
+    "kH":{
+        "type":"product",
+        "a":"kHScaled",
+        "b":"bwPower0p75"},
+    "kI":{
+        "type":"product",
+        "a":"kIScaled",
+        "b":"bwPower0p75"},
+    "kIF":{
+        "type":"product",
+        "a":"kIFScaled",
+        "b":"bwPower0p75"},
+    "kRBC":{
+        "type":"product",
+        "a":"kRBCScaled",
+        "b":"bwPower0p75"},
+    "kR":{
+        "type":"product",
+        "a":"kRScaled",
+        "b":"bwPower0p75"},
+    "kU":{
+        "type":"product",
+        "a":"kUScaled",
+        "b":"bwPower0p75"},
+    "dBL":{
+        "type":"product",
+        "a":"dBLPaper",
+        "b":"plasmaVolume"},
+    "dBBr":{
+        "type":"product",
+        "a":"dBBrPaper",
+        "b":"plasmaVolume"},
+    "kLB:I":{
+        "type":"product",
+        "a":"kLB:IPaper",
+        "b":"liverVolume"},
+    "kBK:I":{
+        "type":"product",
+        "a":"kBK:IPaper",
+        "b":"plasmaVolume"},
+    "kKB:I":{
+        "type":"product",
+        "a":"kKB:IPaper",
+        "b":"kidneyVolume"},
+    "kKU:I":{
+        "type":"product",
+        "a":"kKU:IPaper",
+        "b":"kidneyVolume"},
+    "kBH:I":{
+        "type":"product",
+        "a":"kBH:IPaper",
+        "b":"plasmaVolume"},
+    "kBU:I":{
+        "type":"product",
+        "a":"kBU:IPaper",
+        "b":"plasmaVolume"},
+    "kBF:I":{
+        "type":"product",
+        "a":"kBF:IPaper",
+        "b":"plasmaVolume"},
+    "kLF:I":{
+        "type":"product",
+        "a":"kLF:IPaper",
+        "b":"liverVolume"},
+    "kBBr:I":{
+        "type":"product",
+        "a":"kBBr:IPaper",
+        "b":"plasmaVolume"},
+    "kBrB:I":{
+        "type":"product",
+        "a":"kBrB:IPaper",
+        "b":"brainVolume"}}
+}

pythonScripts/cModel.py

@@ -370,6 +370,7 @@ class model:
       pars=self.parSetup['parameters']
       pars['one']={'value':1}
       pars['zero']={'value':0}
+      pars['two']={'value':2}
    
 
    def M(self,t,y=numpy.array([])):