slv-utils
Version:
Utilities for working with SLV and DAT files.
1,938 lines (1,937 loc) • 569 kB
JSON
{
"sourceFormat": "SLV",
"content": {
"header": "DBSolve Optimum (new parser) 1 Jul 2006\nSLV25.00*",
"map": [
{
"key": "Number of rows in matrix (Number of activities) ",
"rawValue": [
"8 "
],
"parsedValue": [
{
"type": "number",
"value": 8
}
]
},
{
"key": "Number of cols in matrix (Number of compounds) ",
"rawValue": [
"7 "
],
"parsedValue": [
{
"type": "number",
"value": 7
}
]
},
{
"key": "Initial System dimension ",
"rawValue": [
"6 "
],
"parsedValue": [
{
"type": "number",
"value": 6
}
]
},
{
"key": "Selected Variable(Always TIME for ODE) ",
"rawValue": [
"7 "
],
"parsedValue": [
{
"type": "number",
"value": 7
}
]
},
{
"key": "Maximum Value of the Selected Variable ",
"rawValue": [
"2.000000e+04 "
],
"parsedValue": [
{
"type": "number",
"value": 20000
}
]
},
{
"key": "Minimum Value of the Selected Variable ",
"rawValue": [
"0.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "Initial Step ",
"rawValue": [
"1.000000e-03 "
],
"parsedValue": [
{
"type": "number",
"value": 0.001
}
]
},
{
"key": "Method Accuracy ",
"rawValue": [
"1.000000e-05 "
],
"parsedValue": [
{
"type": "number",
"value": 0.00001
}
]
},
{
"key": "Maximum Number of Method Steps ",
"rawValue": [
"10000 "
],
"parsedValue": [
{
"type": "number",
"value": 10000
}
]
},
{
"key": "1st Variale for plotting ",
"rawValue": [
"X[0] "
],
"parsedValue": [
{
"type": "string",
"value": "X[0]"
}
]
},
{
"key": "2nd Variable for plotting: ",
"rawValue": [
"X[1] "
],
"parsedValue": [
{
"type": "string",
"value": "X[1]"
}
]
},
{
"key": "1st Value Maximum for plotting ",
"rawValue": [
"1.000000e+02 "
],
"parsedValue": [
{
"type": "number",
"value": 100
}
]
},
{
"key": "1st Value Minimum for plotting ",
"rawValue": [
"0.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "2nd Value Maximum for plotting ",
"rawValue": [
"1.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "2nd Value Minimum for plotting ",
"rawValue": [
"0.000000e+00 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "Distance between Plotting points ",
"rawValue": [
"1.000000e+02 "
],
"parsedValue": [
{
"type": "number",
"value": 100
}
]
},
{
"key": "Step for Numerical derivation ",
"rawValue": [
"1.000000e-05 "
],
"parsedValue": [
{
"type": "number",
"value": 0.00001
}
]
},
{
"key": "(Internal) DbsolveStep WWW Demo ",
"rawValue": [
"2122 "
],
"parsedValue": [
{
"type": "number",
"value": 2122
}
]
},
{
"key": "Elementary Constant ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "FileOutput ",
"rawValue": [
"0 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "TextOutput ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "DrawOutput ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "TransferLast ",
"rawValue": [
"0 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "Stoichiometric Matrix ",
"rawValue": [
"1 1 1 \n1 4 -1 \n1 6 -1 \n1 7 1 \n2 1 -1 \n2 2 1 \n2 5 1 \n3 2 -1 \n3 3 1 \n3 6 -1 \n3 7 1 \n4 3 -1 \n4 4 1 \n5 1 -1 \n6 6 1 \n6 7 -1 \n7 3 1 \n7 5 -1 \n8 5 -1 \n0 0 0.0 \n& "
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]
},
{
"key": "Elementary Constants ",
"rawValue": [
"1.944853e+00 1.931480e+00 1.738867e+00 1.541431e+00 1.507216e+00 1.000000e+01 1.766963e+00 5.000000e+00 1.071796e+00 1.002559e+00 "
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"parsedValue": [
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},
{
"key": "Initial concentrations ",
"rawValue": [
"1.581402e+00 1.657051e+00 1.740312e+00 1.153910e+00 1.926045e+00 1.076286e+00 1.147163e+00 "
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}
]
},
{
"key": "Initial Stiffness",
"rawValue": [
"0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 "
],
"parsedValue": [
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},
{
"key": "Initial Family Steps",
"rawValue": [
"1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 "
],
"parsedValue": [
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},
{
"key": "Number of fitting parameters (Old Income Flux Constant Number) ",
"rawValue": [
"50 "
],
"parsedValue": [
{
"type": "number",
"value": 50
}
]
},
{
"key": "Number of scan parameters ",
"rawValue": [
"50 "
],
"parsedValue": [
{
"type": "number",
"value": 50
}
]
},
{
"key": "ABsolute Fitting ",
"rawValue": [
"0 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "Variables for FileOutput ",
"rawValue": [
"V[2] V[5] X[3] X[4] X[5] X[6] X[7] #### "
],
"parsedValue": [
{
"type": "strings",
"value": [
"V[2]",
"",
"V[5]",
"",
"X[3]",
"",
"X[4]",
"",
"X[5]",
"",
"X[6]",
"",
"X[7]",
"",
"",
"",
"####"
]
}
]
},
{
"key": "Variables for FileOutputOn ",
"rawValue": [
" #### "
],
"parsedValue": [
{
"type": "strings",
"value": [
"####"
]
}
]
},
{
"key": "(Internal) Temporary Print Option ",
"rawValue": [
"0 "
],
"parsedValue": [
{
"type": "number",
"value": 0
}
]
},
{
"key": "LeastFitting ",
"rawValue": [
"1 "
],
"parsedValue": [
{
"type": "number",
"value": 1
}
]
},
{
"key": "Output File Name ",
"rawValue": [
"ma.out "
],
"parsedValue": [
[
{
"type": "string",
"value": "ma"
},
{
"type": "strings",
"value": [
".out"
]
}
]
]
},
{
"key": "Experimental Data File Name ",
"rawValue": [
"pw.dat "
],
"parsedValue": [
[
{
"type": "string",
"value": "pw"
},
{
"type": "strings",
"value": [
".dat"
]
}
]
]
},
{
"key": "\nRight Hand Sides && \nInitial Values && \nComments Or Selkov DB record",
"rawValue": [
"\n//! Pools \nCoA=-AcCoA+Pool[1];// for CoA+AcCoA \n//! Rate laws \n//i_isl=P[1]; \n//i_ms=P[2]; \nV[1]=Vm_1*(OA*AcCoA-ICit*CoA/Keq_1)/(Km_OA_1+OA+(Km_OA_1/Km_ICit_1)*ICit); \nV[2]=(1-i_icl/100)*Vm_2*(ICit-Suc*GlOx/Keq_2)/(Km_ICit_2+ICit)/(1+Suc/Ki_Suc_2)/(1+Mal/Ki_Mal_2); \nV[3]=(1-i_ms/100)*Vm_3*(GlOx*AcCoA-Mal*CoA/Keq_3)/(Km_GlOx_3+GlOx+(Km_GlOx_3/Km_Mal_3)*Mal); \nV[4]=Vm_4*(Mal*NAD-OA*NADH/Keq_4)/(Km_Mal_4+Mal+(Km_Mal_4/Km_OA_4)*OA); \nV[5]=Vm_5*ICit*NADP/(Km_ICit_5+ICit)/(1+GlOx/Ki_GlOx_5)/(1+OA/Ki_OA_5); \nV[6]=k6*CoA; \nV[7]=Vm_7*(Suc-Mal/Keq_7)/(Km_Suc_7+Suc+(Km_Suc_7/Km_Mal_7)*Mal); \nV[8]=k8*Suc; \n//! Differential equations \n//for ICit \nF[1]=V[1]-V[2]-V[5]; \n//for GlOx \nF[2]=V[2]-V[3]; \n//for Mal \nF[3]=V[3]-V[4]+V[7]; \n//for OA \nF[4]=-V[1]+V[4]; \n//for Suc \nF[5]=V[2]-V[7]-V[8]; \n//for AcCoA \nF[6]=-V[1]-V[3]+V[6]; \n//for CoA \nF[7]=V[1]+V[3]-V[6]; \n//! Explicit functions ",
"\n//! Data comments \n//! Compound administration \n//! Compound action on target \n//! Auxiliary parameters \n//! Compartment volumes \n//! Initial concentrations \nICit=1; \nGlOx=1; \nMal=1; \nOA=1; \nSuc=1; \nAcCoA=2; \nCoA=1; \n//! Kinetic parameters \n//********************************* \ni_icl=55.5;//0; \ni_ms=80;//0; \n//********************************* \nVm_1=50;// fp \nKeq_1=10;//fp \nKm_OA_1=0.04;// ec \nKm_ICit_1=1;//fp \n//******************************** \nVm_2=30; \nKeq_2=10; \nKm_ICit_2=0.145; \nKi_Suc_2=5; \nKi_Mal_2=5; \n//******************************** \nVm_3=50;//fp \nKeq_3=10;//fp \nKm_GlOx_3=0.02; \nKm_Mal_3=1;//fp \n//******************************** \nVm_4=50;//fp \nKeq_4=10;//fp \nKm_Mal_4=0.3;//ec \nKm_OA_4=0.06;//ec \n//******************************** \nVm_5=14;//70 \nKm_ICit_5=0.07; \nKi_GlOx_5=0.5;//fp \nKi_OA_5=0.5;//fp \n//********************************** \nk6=10;//10;//fp \n//********************************* \nVm_7=20;//fp \nKeq_7=1;//fp \nKm_Suc_7=0.2;//fp \nKm_Mal_7=0.1;//fp \n//*********************************** \nk8=5;//5;//fp \n//! Buffered concentrations \nNAD=2; \nNADH=1; \nNADP=2; \n//! Parameters for fitting \ni_icl=49; \ni_ms=70; \n// \ni_ms=0; \ni_icl=30.7; \nICit=1.044872e+00; \nGlOx=9.845177e-01; \nMal=1.039410e+00; \nOA=1.300135e+00; \nSuc=1.503710e+00; \nAcCoA=4.442447e-01; \nCoA=2.240200e+00; \n//! Pools initial \n//Pool[1]=3;//CoA+AcCoA \nPool[1]=CoA+AcCoA; ",
"\n\n#dbs# "
],
"parsedValue": [
[
{
"type": "lineComment",
"header": 1,
"value": " Pools ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "CoA",
"rhs": "-AcCoA+Pool[1]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " for CoA+AcCoA ",
"newLine": false
},
{
"type": "lineComment",
"header": 1,
"value": " Rate laws ",
"newLine": true
},
{
"type": "lineComment",
"header": 0,
"value": "i_isl=P[1]; ",
"newLine": true
},
{
"type": "lineComment",
"header": 0,
"value": "i_ms=P[2]; ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "V[1]",
"rhs": "Vm_1*(OA*AcCoA-ICit*CoA/Keq_1)/(Km_OA_1+OA+(Km_OA_1/Km_ICit_1)*ICit)",
"newLine": true
}
},
{
"type": "expression",
"value": {
"lhs": "V[2]",
"rhs": "(1-i_icl/100)*Vm_2*(ICit-Suc*GlOx/Keq_2)/(Km_ICit_2+ICit)/(1+Suc/Ki_Suc_2)/(1+Mal/Ki_Mal_2)",
"newLine": true
}
},
{
"type": "expression",
"value": {
"lhs": "V[3]",
"rhs": "(1-i_ms/100)*Vm_3*(GlOx*AcCoA-Mal*CoA/Keq_3)/(Km_GlOx_3+GlOx+(Km_GlOx_3/Km_Mal_3)*Mal)",
"newLine": true
}
},
{
"type": "expression",
"value": {
"lhs": "V[4]",
"rhs": "Vm_4*(Mal*NAD-OA*NADH/Keq_4)/(Km_Mal_4+Mal+(Km_Mal_4/Km_OA_4)*OA)",
"newLine": true
}
},
{
"type": "expression",
"value": {
"lhs": "V[5]",
"rhs": "Vm_5*ICit*NADP/(Km_ICit_5+ICit)/(1+GlOx/Ki_GlOx_5)/(1+OA/Ki_OA_5)",
"newLine": true
}
},
{
"type": "expression",
"value": {
"lhs": "V[6]",
"rhs": "k6*CoA",
"newLine": true
}
},
{
"type": "expression",
"value": {
"lhs": "V[7]",
"rhs": "Vm_7*(Suc-Mal/Keq_7)/(Km_Suc_7+Suc+(Km_Suc_7/Km_Mal_7)*Mal)",
"newLine": true
}
},
{
"type": "expression",
"value": {
"lhs": "V[8]",
"rhs": "k8*Suc",
"newLine": true
}
},
{
"type": "lineComment",
"header": 1,
"value": " Differential equations ",
"newLine": true
},
{
"type": "lineComment",
"header": 0,
"value": "for ICit ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[1]",
"rhs": "V[1]-V[2]-V[5]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "for GlOx ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[2]",
"rhs": "V[2]-V[3]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "for Mal ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[3]",
"rhs": "V[3]-V[4]+V[7]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "for OA ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[4]",
"rhs": "-V[1]+V[4]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "for Suc ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[5]",
"rhs": "V[2]-V[7]-V[8]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "for AcCoA ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[6]",
"rhs": "-V[1]-V[3]+V[6]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "for CoA ",
"newLine": true
},
{
"type": "expression",
"value": {
"lhs": "F[7]",
"rhs": "V[1]+V[3]-V[6]",
"newLine": true
}
},
{
"type": "lineComment",
"header": 1,
"value": " Explicit functions",
"newLine": true
}
],
[
{
"type": "lineComment",
"header": 1,
"value": " Data comments ",
"newLine": true
},
{
"type": "lineComment",
"header": 1,
"value": " Compound administration ",
"newLine": true
},
{
"type": "lineComment",
"header": 1,
"value": " Compound action on target ",
"newLine": true
},
{
"type": "lineComment",
"header": 1,
"value": " Auxiliary parameters ",
"newLine": true
},
{
"type": "lineComment",
"header": 1,
"value": " Compartment volumes ",
"newLine": true
},
{
"type": "lineComment",
"header": 1,
"value": " Initial concentrations ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "ICit",
"rhs": "1",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "GlOx",
"rhs": "1",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Mal",
"rhs": "1",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "OA",
"rhs": "1",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Suc",
"rhs": "1",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "AcCoA",
"rhs": "2",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "CoA",
"rhs": "1",
"newLine": true
}
},
{
"type": "strings",
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""
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},
{
"type": "lineComment",
"header": 1,
"value": " Kinetic parameters ",
"newLine": true
},
{
"type": "lineComment",
"header": 0,
"value": "********************************* ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "i_icl",
"rhs": "55.5",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "0; ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "i_ms",
"rhs": "80",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "0; ",
"newLine": false
},
{
"type": "lineComment",
"header": 0,
"value": "********************************* ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "Vm_1",
"rhs": "50",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " fp ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "Keq_1",
"rhs": "10",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "fp ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "Km_OA_1",
"rhs": "0.04",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": " ec ",
"newLine": false
},
{
"type": "numeric",
"value": {
"lhs": "Km_ICit_1",
"rhs": "1",
"newLine": true
}
},
{
"type": "lineComment",
"header": 0,
"value": "fp ",
"newLine": false
},
{
"type": "lineComment",
"header": 0,
"value": "******************************** ",
"newLine": true
},
{
"type": "numeric",
"value": {
"lhs": "Vm_2",
"rhs": "30",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Keq_2",
"rhs": "10",
"newLine": true
}
},
{
"type": "numeric",
"value": {
"lhs": "Km_ICit_2",
"rhs": "0.145",
"newLine": true
}
},
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