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adding Diazepam, in cotinine, clearance is 10x what is referenced in paper

Andrej 2 years ago
parent
commit
ddb428d8cb
3 changed files with 260 additions and 10 deletions
  1. 3 2
      models/cCotinine.json
  2. 109 0
      models/cDiazepam.json
  3. 148 8
      pythonScripts/compartmentModel.ipynb

+ 3 - 2
models/cCotinine.json

@@ -33,9 +33,10 @@
       "(arterial,venous):testes":"testesFlow",
       "(arterial,venous):remainder":"remainderFlow"},
    "commentSources":"constants in concentration units per s",
+   "commentHeavyside":"value is mass of exogene/volume of container/duration",
    "sources":{
       "arterial":{"name":"exponential","k":-0.005,"constant":0},
-      "venous":{"name":"Heavyside","limit":30,"value":1.22e3}},
+      "venous":{"name":"Heavyside","limit":3,"value":1.22e4}},
    "commentBindings":"split to flow and diffusion dominated",
    "bindings": {
       "flowComments":"group common sources or targets with brackets",
@@ -103,6 +104,6 @@
         "venousVolume":{"value":13.6,"unit":"g"},
         "arterialVolume":{"value":6.8,"unit":"g"},
         "liverToExcrementNotes":"CL=0.13 ml/min,PC=0.39,f=0.97,V=11g->k1=0.00049/s",
-        "k1":{"value":0.0105,"unit":"1/s"}}
+        "k1":{"value":0.0049,"unit":"1/s"}}
 
 }

+ 109 - 0
models/cDiazepam.json

@@ -0,0 +1,109 @@
+{
+   "compartments":["adipose","brain","heart","kidney","liver",
+   "splanchnic","stomach","muscle","skin","testes","remainder","lung",
+   "excrement","arterial","venous","source"],
+   "commentParameters":"every parameter must have a value, name is optional and used in SE computation",
+   "volumes":{
+      "adipose":"adiposeVolume",
+      "brain":"brainVolume",
+      "heart":"heartVolume",
+      "kidney":"kidneyVolume",
+      "liver":"liverVolume",
+      "lung":"lungVolume",
+      "muscle":"muscleVolume",
+      "skin":"skinVolume",
+      "splanchnic":"splanchnicVolume",
+      "stomach":"stomachVolume",
+      "testes":"testesVolume",
+      "remainder":"remainderVolume",
+      "venous":"venousVolume",
+      "arterial":"arterialVolume"},
+   "flows":{
+      "(arterial,venous):adipose":"adiposeFlow",
+      "(arterial,venous):brain":"brainFlow",
+      "(arterial,venous):heart":"heartFlow",
+      "(arterial,venous):kidney":"kidneyFlow",
+      "arterial:liver":"liverInFlow",
+      "liver:venous":"liverOutFlow",
+      "(arterial,venous):lung":"totalFlow",
+      "(arterial,venous):muscle":"muscleFlow",
+      "(arterial,venous):skin":"skinFlow",
+      "(arterial,liver):splanchnic":"splanchnicFlow",
+      "(arterial,liver):stomach":"stomachFlow",
+      "(arterial,venous):testes":"testesFlow",
+      "(arterial,venous):remainder":"remainderFlow"},
+   "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 brackets",
+      "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"],
+      "diffusion":{
+         "liver->excrement":"k1"}},
+    "pcComments":"always related to outflow of organs", 
+    "partitionCoefficients":{
+       "adipose":"adiposePC",
+       "brain":"brainPC",
+       "heart":"heartPC",
+       "kidney":"kidneyPC",
+       "liver":"liverPC",
+       "lung":"lungPC",
+       "muscle":"musclePC",
+       "remainder":"remainderPC",
+       "skin":"skinPC",
+       "splanchnic":"splanchnicPC",
+       "stomach":"stomachPC",
+       "testes":"testesPC"},
+     "parameters":{
+        "adiposePC":{"value":23.1,"dist":"lognormal","cv":0.3},
+	     "brainPC":{"value":2.2,"dist":"lognormal","cv":0.3},
+	     "heartPC":{"value":4.3},
+        "kidneyPC":{"value":5.2},
+	     "liverPC":{"value":9.1},
+	     "lungPC":{"value":5.3},
+	     "musclePC":{"value":2.4},
+        "remainderPC":{"value":16.5},
+        "skinPC":{"value":3.2,"dist":"lognormal","cv":0.3},
+	     "splanchnicPC":{"value":4.3},
+	     "stomachPC":{"value":4.5},
+	     "testesPC":{"value":4.7},
+        "flowNotes":"liverOutFlow is sum of liver,splanchnic and stomach",
+        "flowNotes1":"liverOutFlow=3.55+20.25+1.9",
+        "adiposeFlow":{"value":2.55,"unit":"ml/min"},
+        "brainFlow":{"value":0.78,"unit":"ml/min"},
+        "heartFlow":{"value":4.2,"unit":"ml/min"},
+        "kidneyFlow":{"value":16.61,"unit":"ml/min"},
+        "liverInFlow":{"value":3.55,"unit":"ml/min"},
+        "liverOutFlow":{"value":25.7,"unit":"ml/min"},
+        "totalFlow":{"value":80,"unit":"ml/min"},
+        "muscleFlow":{"value":16.25,"unit":"ml/min"},
+        "skinFlow":{"value":7.1,"unit":"ml/min"},
+        "splanchnicFlow":{"value":20.25,"unit":"ml/min"},
+        "stomachFlow":{"value":1.9,"unit":"ml/min"},
+        "testesFlow":{"value":1.9,"unit":"ml/min"},
+        "remainderFlow":{"value":4.91,"unit":"ml/min"},
+        "adiposeVolume":{"value":10,"unit":"g"},
+        "brainVolume":{"value":1.2,"unit":"g"},
+        "heartVolume":{"value":1,"unit":"g"},
+        "kidneyVolume":{"value":2,"unit":"g"},
+        "liverVolume":{"value":11,"unit":"g"},
+        "lungVolume":{"value":1.2,"unit":"g"},
+        "muscleVolume":{"value":125,"unit":"g"},
+        "skinVolume":{"value":43.8,"unit":"g"},
+        "splanchnicVolume":{"value":15,"unit":"g"},
+        "stomachVolume":{"value":1.1,"unit":"g"},
+        "testesVolume":{"value":2.5,"unit":"g"},
+        "remainderVolume":{"value":15.8,"unit":"g"},
+        "venousVolume":{"value":13.6,"unit":"g"},
+        "arterialVolume":{"value":6.8,"unit":"g"},
+        "liverToExcrementNotes":"CL=422 ml/min,PC=9.1,f=0.15,V=11g->k1=0.0105/s",
+        "k1":{"value":0.0105,"unit":"1/s"}}
+
+}

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+ 148 - 8
pythonScripts/compartmentModel.ipynb


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