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Inulin.json
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{
"Version": 79,
"Individuals": [
{
"Name": "Rat",
"Seed": 24116796,
"OriginData": {
"CalculationMethods": [
"SurfaceAreaPlsInt_VAR1"
],
"Species": "Rat"
},
"Parameters": [
{
"Path": "Organism|Bone|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Brain|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Fat|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Gonads|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Heart|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Kidney|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|LargeIntestine|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|LargeIntestine|Mucosa|Caecum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|LargeIntestine|Mucosa|ColonAscendens|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|LargeIntestine|Mucosa|ColonDescendens|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|LargeIntestine|Mucosa|ColonSigmoid|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|LargeIntestine|Mucosa|ColonTransversum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|LargeIntestine|Mucosa|Rectum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Liver|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Lung|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Muscle|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Pancreas|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Skin|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|SmallIntestine|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|SmallIntestine|Mucosa|Duodenum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|SmallIntestine|Mucosa|LowerIleum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|SmallIntestine|Mucosa|LowerJejunum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|SmallIntestine|Mucosa|UpperIleum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|SmallIntestine|Mucosa|UpperJejunum|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Spleen|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
},
{
"Path": "Organism|Stomach|Fraction of blood for sampling",
"Value": 0.18,
"ValueOrigin": {
"Source": "Publication",
"Description": "Niederalt2018 (doi: 10.1007/s10928-017-9559-4)"
}
}
],
"ExpressionProfiles": []
}
],
"Compounds": [
{
"Name": "Inulin",
"IsSmallMolecule": true,
"Lipophilicity": [
{
"Name": "Measurement",
"Parameters": [
{
"Name": "Lipophilicity",
"Value": -10.0,
"Unit": "Log Units",
"ValueOrigin": {
"Source": "Other",
"Description": "Highly hydrophilic"
}
}
]
}
],
"FractionUnbound": [
{
"Name": "Measurement",
"Species": "Human",
"Parameters": [
{
"Name": "Fraction unbound (plasma, reference value)",
"Value": 1.0,
"ValueOrigin": {
"Source": "Other",
"Description": "Assumption"
}
}
]
}
],
"Solubility": [
{
"Name": "Measurement",
"Parameters": [
{
"Name": "Solubility at reference pH",
"Value": 9999.0,
"Unit": "mg/l",
"ValueOrigin": {
"Source": "Other",
"Description": "/Dummy value not used in the simulation"
}
},
{
"Name": "Reference pH",
"Value": 7.0,
"ValueOrigin": {
"Source": "Other",
"Description": "/Dummy value not used in the simulation"
}
}
]
}
],
"Processes": [
{
"InternalName": "GlomerularFiltration",
"DataSource": "GFR",
"Species": "Human",
"Parameters": [
{
"Name": "GFR fraction",
"Value": 1.0,
"ValueOrigin": {
"Source": "Publication",
"Method": "Other",
"Description": "Tsuji1983 (DOI: 10.1002/jps.2600721103)"
}
}
]
}
],
"CalculationMethods": [
"Cellular partition coefficient method - PK-Sim Standard",
"Cellular permeability - PK-Sim Standard"
],
"Parameters": [
{
"Name": "Molecular weight",
"Value": 5500.0,
"Unit": "g/mol",
"ValueOrigin": {
"Source": "Publication",
"Description": "Ohno1978"
}
},
{
"Name": "Radius (solute)",
"Value": 0.00139,
"Unit": "µm",
"ValueOrigin": {
"Id": 26,
"Source": "Publication",
"Description": "Ghandehari1997"
}
},
{
"Name": "Kd (FcRn) in endosomal space",
"Value": 999999.0,
"Unit": "µmol/l",
"ValueOrigin": {
"Id": 26,
"Source": "Other",
"Description": "high value representing no FcRn binding"
}
}
]
}
],
"Protocols": [
{
"Name": "20mgkg_IV",
"ApplicationType": "Intravenous",
"DosingInterval": "Single",
"Parameters": [
{
"Name": "Start time",
"Value": 0.0,
"Unit": "h"
},
{
"Name": "InputDose",
"Value": 20.0,
"Unit": "mg/kg"
},
{
"Name": "Infusion time",
"Value": 5.0,
"Unit": "s"
}
]
},
{
"Name": "200mgkg_IV",
"ApplicationType": "Intravenous",
"DosingInterval": "Single",
"Parameters": [
{
"Name": "Start time",
"Value": 0.0,
"Unit": "h"
},
{
"Name": "InputDose",
"Value": 200.0,
"Unit": "mg/kg"
},
{
"Name": "Infusion time",
"Value": 5.0,
"Unit": "s"
}
]
}
],
"Simulations": [
{
"Name": "Inulin_20mgkg",
"Model": "TwoPores",
"ObservedData": [
"Tsuji1983_PBPK_Antibiotics_PKSimImport.Lung.20",
"Tsuji1983_PBPK_Antibiotics_PKSimImport.Bone.20",
"Tsuji1983_PBPK_Antibiotics_PKSimImport.Muscle.20",
"Tsuji1983_PBPK_Antibiotics_PKSimImport.Gut.20",
"Tsuji1983_PBPK_Antibiotics_PKSimImport.Heart.20",
"Tsuji1983_PBPK_Antibiotics_PKSimImport.VenousBlood.Plasma.20",
"Tsuji1983_PBPK_Antibiotics_PKSimImport.Skin.20"
],
"Solver": {},
"OutputSchema": [
{
"Parameters": [
{
"Name": "Start time",
"Value": 0.0,
"Unit": "h"
},
{
"Name": "End time",
"Value": 3.0,
"Unit": "h",
"ValueOrigin": {
"Source": "Unknown"
}
},
{
"Name": "Resolution",
"Value": 120.0,
"Unit": "pts/h",
"ValueOrigin": {
"Source": "Unknown"
}
}
]
}
],
"Parameters": [
{
"Path": "Applications|20mgkg_IV|Application_1|ProtocolSchemaItem|Infusion time",
"Value": 0.0833333333,
"Unit": "min"
}
],
"OutputSelections": [
"Organism|VenousBlood|Plasma|Inulin|Concentration in container",
"Organism|Lung|Inulin|Whole Organ",
"Organism|Muscle|Inulin|Whole Organ",
"Organism|Bone|Inulin|Whole Organ",
"Organism|Heart|Inulin|Whole Organ",
"Organism|Skin|Inulin|Whole Organ",
"Organism|SmallIntestine|Inulin|Whole Organ (Small Intestine)",
"Organism|SmallIntestine|Inulin|Whole Organ (Small Intestine) incl. FcRn_Complex-Inulin",
"Organism|LargeIntestine|Inulin|Whole Organ (Large Intestine)",
"Organism|LargeIntestine|Inulin|Whole Organ (Large Intestine) incl. FcRn_Complex-Inulin"
],
"OutputMappings": [
{
"Scaling": "Log",
"Path": "Inulin_20mgkg|Organism|VenousBlood|Plasma|Inulin|Concentration in container",
"ObservedData": "Tsuji1983_PBPK_Antibiotics_PKSimImport.VenousBlood.Plasma.20"
},
{
"Scaling": "Log",
"Path": "Inulin_20mgkg|Organism|Bone|Inulin|Whole Organ",
"ObservedData": "Tsuji1983_PBPK_Antibiotics_PKSimImport.Bone.20"
},
{
"Scaling": "Log",
"Path": "Inulin_20mgkg|Organism|Heart|Inulin|Whole Organ",
"ObservedData": "Tsuji1983_PBPK_Antibiotics_PKSimImport.Heart.20"
},
{
"Scaling": "Log",
"Path": "Inulin_20mgkg|Organism|Lung|Inulin|Whole Organ",
"ObservedData": "Tsuji1983_PBPK_Antibiotics_PKSimImport.Lung.20"
},
{
"Scaling": "Log",
"Path": "Inulin_20mgkg|Organism|Muscle|Inulin|Whole Organ",
"ObservedData": "Tsuji1983_PBPK_Antibiotics_PKSimImport.Muscle.20"
},
{
"Scaling": "Log",
"Path": "Inulin_20mgkg|Organism|Skin|Inulin|Whole Organ",
"ObservedData": "Tsuji1983_PBPK_Antibiotics_PKSimImport.Skin.20"
}
],
"Individual": "Rat",
"Compounds": [
{
"Name": "Inulin",
"CalculationMethods": [
"Cellular partition coefficient method - PK-Sim Standard",
"Cellular permeability - PK-Sim Standard"
],
"Processes": [
{
"Name": "Glomerular Filtration-GFR",
"SystemicProcessType": "GFR"
}
],
"Protocol": {
"Name": "20mgkg_IV"
}
}
],
"HasResults": true,
"IndividualAnalyses": [
{
"Axes": [
{
"Unit": "h",
"Dimension": "Time",
"Type": "X",
"GridLines": false,
"Visible": true,
"DefaultColor": "#FFFFFF",
"DefaultLineStyle": "None",
"Scaling": "Linear",
"NumberMode": "Normal"
},
{
"Unit": "µmol/l",
"Dimension": "Concentration (molar)",
"Type": "Y",
"GridLines": false,
"Visible": true,
"DefaultColor": "#FFFFFF",
"DefaultLineStyle": "Solid",
"Scaling": "Linear",
"NumberMode": "Normal"
}
],
"Curves": [
{
"Name": "Inulin-Venous Blood-Plasma-Concentration",
"X": "Time",
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