Adjusting model parameters to include source term, setting values in l/hour units

models/humanHG.json

@@ -11,7 +11,7 @@
    "volumeComment":"in a compartment w/o volume, value is mass",
    "volumes":{
       "plasma":"plasmaVolume",
-      "venous":"plasmaVolume",
+      "venous":"venousVolume",
       "kidney":"kidneyVolume",
       "richlyPerfused":"richlyPerfusedVolume",
       "fat":"fatVolume",
@@ -35,8 +35,8 @@
       "plasma:venous":"plasmaFlow"},
    "commentSources":"constants in concentration units per s",
    "commentHeavyside":"value is mass of exogene/volume of container/duration",
-   "sources":{
-      "intestine":{"name":"constant","value":0.0486,"unit":"ug/min"}},
+   "inputs":{
+      "intestine":"oralIngestion"},
    "commentBindings":"split to flow and diffusion dominated",
    "bindings": {
       "flowComments":"group common sources or targets with brackets",

models/humanHG_parameters1.json

@@ -1,6 +1,8 @@
 {"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",
         "brainBloodPC":{"value":1,"dist":"lognormal","cv":0.3},
         "brainPC":{"value":3,"dist":"lognormal","cv":0.3},
@@ -37,6 +39,7 @@
         "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"},
@@ -48,7 +51,8 @@
         "gutVolume":{"derived":"gutVolume"},
         "intestineVolume":{"derived":"intestineVolume"},
         "commentFractions":"X",
-        "plasmaVolumeFraction":{"value":0.024,"dist":"normal","cv":0.14},
+        "plasmaVolumeFraction":{"value":0.012,"dist":"normal","cv":0.14},
+        "venousVolumeFraction":{"value":0.012,"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},
@@ -74,10 +78,10 @@
         "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":1.67e-6,"unit":"l/min","dist":"lognormal","cv":0.3},
-        "kFScaled":{"value":3.33e-6,"unit":"l/min","dist":"lognormal","cv":0.36},
-        "kHScaled":{"value":1.17e-7,"unit":"l/min","dist":"lognormal","cv":0.25},
-        "kIScaled":{"value":1.67e-5,"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},
@@ -133,6 +137,10 @@
            "type":"product",
            "a":"plasmaVolumeFraction",
            "b":"bodyWeight"},
+        "venousVolume":{
+           "type":"product",
+           "a":"venousVolumeFraction",
+           "b":"bodyWeight"},
         "redBloodCellsVolume":{
            "type":"product",
            "a":"redBloodCellsVolumeFraction",

models/humanHGplusI.json

@@ -12,7 +12,7 @@
    "volumeComment":"in a compartment w/o volume, value is mass",
    "volumes":{
       "plasma":"plasmaVolume",
-      "venous":"plasmaVolume",
+      "venous":"venousVolume",
       "kidney":"kidneyVolume",
       "richlyPerfused":"richlyPerfusedVolume",
       "fat":"fatVolume",
@@ -40,8 +40,8 @@
       "plasma:venous":"plasmaFlow"},
    "commentSources":"constants in concentration units per s",
    "commentHeavyside":"value is mass of exogene/volume of container/duration",
-   "sources":{
-      "intestine":{"name":"constant","value":0.0486,"unit":"ug/min"}},
+   "inputs":{
+      "intestine":"oralIngestion"},
    "commentBindings":"split to flow and diffusion dominated",
    "bindings": {
       "flowComments":"group common sources or targets with brackets",

models/humanHGplusI_parameters.json

@@ -1,6 +1,8 @@
 {"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",
         "brainBloodPC":{"value":1,"dist":"lognormal","cv":0.3},
         "brainPC":{"value":3,"dist":"lognormal","cv":0.3},
@@ -37,6 +39,7 @@
         "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"},
@@ -48,7 +51,8 @@
         "gutVolume":{"derived":"gutVolume"},
         "intestineVolume":{"derived":"intestineVolume"},
         "commentFractions":"X",
-        "plasmaVolumeFraction":{"value":0.024,"dist":"normal","cv":0.14},
+        "plasmaVolumeFraction":{"value":0.012,"dist":"normal","cv":0.14},
+        "venousVolumeFraction":{"value":0.012,"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},
@@ -87,10 +91,10 @@
         "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":1.67e-6,"unit":"l/min","dist":"lognormal","cv":0.3},
-        "kFScaled":{"value":3.33e-6,"unit":"l/min","dist":"lognormal","cv":0.36},
-        "kHScaled":{"value":1.17e-7,"unit":"l/min","dist":"lognormal","cv":0.25},
-        "kIScaled":{"value":1.67e-5,"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},
@@ -159,6 +163,10 @@
            "type":"product",
            "a":"plasmaVolumeFraction",
            "b":"bodyWeight"},
+        "venousVolume":{
+           "type":"product",
+           "a":"venousVolumeFraction",
+           "b":"bodyWeight"},
         "redBloodCellsVolume":{
            "type":"product",
            "a":"redBloodCellsVolumeFraction",