Adding model files

models/cDiazepam.old.json

@@ -0,0 +1,74 @@
+{
+   "compartments":["adipose","brain","heart","kidney","liver",
+   "splanchnic","stomach","muscle","skin","testes","remainder","lung",
+   "excrement","arterial","venous","source"],
+   "volumes":{
+      "unit":"g",
+      "adipose":10,
+      "brain":1.2,
+      "heart":1,
+      "kidney":2,
+      "liver":11,
+      "lung":1.2,
+      "muscle":125,
+      "skin":43.8,
+      "splanchnic":15,
+      "stomach":1.1,
+      "testes":2.5,
+      "remainder":15.8,
+      "venous":13.6,
+      "arterial":6.8},
+   "flowNotes":"liver:arterial is sum of liver,splanchnic and stomach",
+   "flowNotes1":"liver:arterial=3.55+20.25+1.9",
+   "flows":{
+      "unit":"ml/min",
+      "(arterial,venous):adipose":2.55,
+      "(arterial,venous):brain":0.78,
+      "(arterial,venous):heart":4.2,
+      "(arterial,venous):kidney":16.61,
+      "arterial:liver":3.55,
+      "liver:venous":25.7,
+      "(arterial,venous):lung":80,
+      "(arterial,venous):muscle":16.25,
+      "(arterial,venous):skin":7.1,
+      "(arterial,liver):splanchnic":20.25,
+      "(arterial,liver):stomach":1.9,
+      "(arterial,venous):testes":1.9,
+      "(arterial,venous):remainder":4.91,
+      "arterial":80,
+      "venous":80},
+   "commentSources":"constants in concentration units per s",
+   "sources":{
+      "arterial":{"name":"exponential","k":-0.005,"constant":0},
+      "venous":{"name":"Heavyside","limit":300,"value":0.61e2}},
+   "commentBindings":"split to flow and diffusion dominated",
+   "bindings": {
+      "flowComments":"group common sources or targets with braces",
+      "flow":[
+         "(adipose,brain,heart,kidney,liver,muscle,skin,testes,remainder)->venous",
+            
+         "(splanchnic,stomach)->liver",
+         "arterial->(adipose,brain,heart,kidney,liver,muscle,skin,testes,remainder,splanchnic,stomach)",
+         "venous->lung",
+         "lung->arterial"],
+      "diffusionComments":"source->target strength per s",
+      "liverToExcrementNotes":"CL=422ml/min,PC=9.1,f=0.15,V=11g->k=0.0105/s",
+      "sourceToArterialNotes":"ka=0.001/s in paper",
+      "comment:source->venous":0.005,
+      "diffusion":{
+         "liver->excrement":0.0105}},
+    "pcComments":"always related to outflow of organs", 
+    "partitionCoefficients":{
+       "adipose":23.1,
+       "brain":2.2,
+       "heart":4.3,
+       "kidney":5.2,
+       "liver":9.1,
+       "lung":5.3,
+       "muscle":2.4,
+       "remainder":16.5,
+       "skin":3.2,
+       "splanchnic":4.3,
+       "stomach":4.5,
+       "testes":4.7}
+}

models/cModel.json

@@ -0,0 +1,10 @@
+{
+   "compartments":["blood","excrement"],
+   "commentSources":"in units per day",
+   "sources":{
+      "blood":1},
+   "commentBindings":"each gives source->target strength per day",
+   "bindings": {
+      "blood->excrement":0.1}
+   
+}

models/hgModel.json

@@ -0,0 +1,18 @@
+{
+   "compartments":["plasma","intestine","gut","liver","feces","kidney","urine"],
+   "commentSources":"in units per hr",
+   "sources":{
+      "intestine":1},
+   "commentBindings":"each gives source->target strength per hr",
+   "bindings": {
+      "intestine->feces":2e-4,
+      "intestine->gut":5e-3,
+      "gut->liver":0.181,
+      "plasma->liver":0.046,
+      "plasma->gut":0.181,
+      "plasma->kidney":0.175,
+      "liver->intestine":1e-4,
+      "liver->plasma":0.046,
+      "kidney->plasma":0.175,
+      "kidney->urine":1e-9}
+}

models/hgModel1.json

@@ -0,0 +1,15 @@
+{
+   "compartments":["plasma","intestine","gut","liver","feces"],
+   "commentSources":"in units per hr",
+   "sources":{
+      "intestine":1},
+   "commentBindings":"each gives source->target strength per hr",
+   "bindings": {
+      "intestine->feces":2e-4,
+      "intestine->gut":5e-3,
+      "gut->liver":0.181,
+      "plasma->liver":0.046,
+      "plasma->gut":0.181,
+      "liver->intestine":1e-4,
+      "liver->plasma":0.046}
+}

models/humanHG_parameters5.json

@@ -0,0 +1,254 @@
+{"parameters":{
+        "bodyWeight":{"value":67.77,"units":"kg","dist":"lognormal","cv":0.26},
+        "bwPower0p75":{"derived":"bwPower0p75"},
+        "commentPC":"X",
+        "brainBloodPC":{"value":1,"dist":"lognormal","cv":0.3},
+        "brainPC":{"value":3,"dist":"lognormal","cv":0.3},
+        "fatPC":{"value":0.15,"dist":"lognormal","cv":0.3},
+        "gutPC":{"value":1,"dist":"lognormal","cv":0.7},
+        "hairPC":{"derived":"hairPC"},
+        "hairPCBlood":{"value":248.7,"dist":"lognormal","cv":0.7},
+        "kidneyPC":{"value":4.0,"dist":"lognormal","cv":0.3},
+        "liverPC":{"value":5.0,"dist":"lognormal","cv":0.3},
+        "rbcPC":{"value":12.0,"dist":"lognormal","cv":0.3},
+        "richlyPerfusedPC":{"value":1.0,"dist":"lognormal","cv":0.3},
+        "slowlyPerfusedPC":{"value":2.0,"dist":"lognormal","cv":0.3},
+        "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"},
+        "redBloodCellsVolume":{"derived":"redBloodCellsVolume"},
+        "kidneyVolume":{"derived":"kidneyVolume"},
+        "richlyPerfusedVolume":{"derived":"richlyPerfusedVolume"},
+        "fatVolume":{"derived":"fatVolume"},
+        "hairVolume":{"function":"hairGrowth"},
+        "hairGrowthDuration":{"derived":"hairGrowthDuration"},
+        "hairVolumeMax":{"derived":"hairVolumeMax"},
+        "slowlyPerfusedVolume":{"derived":"slowlyPerfusedVolume"},
+        "brainBloodVolume":{"derived":"brainBloodVolume"},
+        "brainVolume":{"derived":"brainVolume"},
+        "liverVolume":{"derived":"liverVolume"},
+        "gutVolume":{"derived":"gutVolume"},
+        "intestineVolume":{"derived":"intestineVolume"},
+        "commentFractions":"X",
+        "plasmaVolumeFraction":{"value":0.024,"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":0.14,"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":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},
+        "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},
+        "heavisideTransition":{"value":100},
+        "hairGrowthStart":{"value":0e6,"unit":"min"},
+        "hairGrowthStop":{"derived":"hairGrowthStop"},
+        "hairGrowth":{"derived":"hairGrowth"}},
+    "functions":{
+       "commentHairGrowth":"2yr hair growth to a total mass of 140g",
+       "hairGrowth":{
+           "type":"linearGrowth",
+           "t1":"hairGrowthStart",
+           "W1":"heavisideTransition",
+           "t2":"hairGrowthStop",
+           "W2":"heavisideTransition",
+           "C":"hairVolumeMax"}},
+    "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"},
+        "plasmaVolume":{
+           "type":"product",
+           "a":"plasmaVolumeFraction",
+           "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"},
+       "hairVolumeMax":{
+           "type":"product",
+           "a":"hairVolumeFraction",
+           "b":"bodyWeight"},
+       "hairGrowthStop":{
+           "type":"sum",
+           "a":"hairGrowthStart",
+           "b":"hairGrowthDuration"},
+       "hairGrowthDuration":{
+            "type":"ratio",
+            "a":"hairVolumeMax",
+            "b":"hairGrowth"},
+       "hairGrowth":{
+            "type":"ratio",
+            "a":"kH",
+            "b":"hairPC"},
+       "hairPC":{
+          "type":"ratio",
+          "a":"hairPCBlood",
+          "b":"slowlyPerfusedPC"},
+       "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_parameters.json

@@ -86,6 +86,7 @@
     "kD":{"derived":"kD"},
     "kF":{"derived":"kF"},
     "kH":{"derived":"kH"},
+    "kHOriginal":{"derived":"kHOriginal"},
     "kI":{"derived":"kI"},
     "kIF":{"derived":"kIF"},
     "kRBC":{"derived":"kRBC"},
@@ -131,7 +132,8 @@
     "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}},
+    "threeQuarters":{"value":0.75},
+    "kHCorrection":{"value":1.67}},
 "derivedParameters":{
     "bwPower0p75":{
         "type":"power",
@@ -303,6 +305,10 @@
         "b":"bwPower0p75"},
     "kH":{
         "type":"product",
+        "a":"kHOriginal",
+        "b":"kHCorrection"},
+    "kHOriginal":{
+        "type":"product",
         "a":"kHScaled",
         "b":"bwPower0p75"},
     "kI":{

setup/setupFast2.json

@@ -0,0 +1,7 @@
+{"method":"LSODA",
+"atol":1e-8,
+"rtol":1e-8,
+"mode":"IVPSimultaneous",
+"nt":201,
+"tmax":2,
+"tUnit":"hour"}

setup/setupFast3.json

@@ -0,0 +1,7 @@
+{"method":"LSODA",
+"atol":1e-8,
+"rtol":1e-8,
+"mode":"IVPSimultaneous",
+"nt":201,
+"tmax":3,
+"tUnit":"hour"}

setup/setupFast4.json

@@ -0,0 +1,7 @@
+{"method":"LSODA",
+"atol":1e-4,
+"rtol":1e-6,
+"mode":"IVPSimultaneous",
+"nt":201,
+"tmax":4,
+"tUnit":"hour"}

setup/setupFast5.json

@@ -0,0 +1,7 @@
+{"method":"LSODA",
+"atol":1e-3,
+"rtol":1e-6,
+"mode":"IVPSimultaneous",
+"nt":201,
+"tmax":5,
+"tUnit":"hour"}