Attachment 'Wambaugh_vLiver_PBPK_based_v4_APAPconj_Glu.xml'

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   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <!-- Created by XMLPrettyPrinter on 10/4/2012 from  -->
   3 <sbml xmlns = "http://www.sbml.org/sbml/level2/version4" level = "2" version = "4">
   4    <model id = "PBPK_model">
   5       <listOfCompartments>
   6          <compartment id = "compartment" size = "1"/>
   7       </listOfCompartments>
   8       <listOfSpecies>
   9          <species id = "CArt" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  10          <species id = "CGut" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  11          <species id = "AGutlumen" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  12          <species id = "CLung" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  13          <species id = "CVen" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  14          <species id = "CRest" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  15          <species id = "CLiver" boundaryCondition = "false" initialConcentration = "1" compartment = "compartment"/>
  16          <species id = "CMetabolized" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  17          <species id = "CKidney" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  18          <species id = "CTubules" boundaryCondition = "false" initialConcentration = "0" compartment = "compartment"/>
  19       </listOfSpecies>
  20       <listOfParameters>
  21          <parameter id = "QGut" value = "69.0144"/>
  22          <parameter id = "VArt" value = "1.49996"/>
  23          <parameter id = "kGutabs" value = "1"/>
  24          <parameter id = "QCardiac" value = "336"/>
  25          <parameter id = "VLung" value = "0.5061"/>
  26          <parameter id = "VVen" value = "3.409"/>
  27          <parameter id = "QRest" value = "174.6192"/>
  28          <parameter id = "Ratioblood2plasma" value = "1"/>
  29          <parameter id = "KRest2plasma" value = "1"/>
  30          <parameter id = "Fraction_unbound_plasma" value = "1"/>
  31          <parameter id = "VRest" value = "33.47204"/>
  32          <parameter id = "QLiver" value = "17.976"/>
  33          <parameter id = "CLmetabolism" value = "0"/>
  34          <parameter id = "Kliver2plasma" value = "1"/>
  35          <parameter id = "VLiver" value = "1.7136"/>
  36          <parameter id = "VGut" value = "1.106"/>
  37          <parameter id = "QKidney" value = "74.3904"/>
  38          <parameter id = "Qgfr" value = "126"/>
  39          <parameter id = "Kkidney2plasma" value = "1"/>
  40          <parameter id = "VKidney" value = "0.2933"/>
  41       </listOfParameters>
  42       <listOfReactions>
  43          <reaction id = "J1" reversible = "false">
  44             <listOfReactants>
  45                <speciesReference species = "CArt" stoichiometry = "1"/>
  46             </listOfReactants>
  47             <listOfProducts>
  48                <speciesReference species = "CGut" stoichiometry = "1"/>
  49             </listOfProducts>
  50             <kineticLaw>
  51                <math xmlns = "http://www.w3.org/1998/Math/MathML">
  52                   <apply>
  53                      <divide/>
  54                      <apply>
  55                         <times/>
  56                         <ci>
  57                               QGut
  58                         </ci>
  59                         <ci>
  60                               CArt
  61                         </ci>
  62                      </apply>
  63                      <ci>
  64                            VArt
  65                      </ci>
  66                   </apply>
  67                </math>
  68             </kineticLaw>
  69          </reaction>
  70          <reaction id = "J2" reversible = "false">
  71             <listOfReactants>
  72                <speciesReference species = "AGutlumen" stoichiometry = "1"/>
  73             </listOfReactants>
  74             <listOfProducts>
  75                <speciesReference species = "CGut" stoichiometry = "1"/>
  76             </listOfProducts>
  77             <kineticLaw>
  78                <math xmlns = "http://www.w3.org/1998/Math/MathML">
  79                   <apply>
  80                      <times/>
  81                      <ci>
  82                            kGutabs
  83                      </ci>
  84                      <ci>
  85                            AGutlumen
  86                      </ci>
  87                   </apply>
  88                </math>
  89             </kineticLaw>
  90          </reaction>
  91          <reaction id = "J3" reversible = "false">
  92             <listOfReactants>
  93                <speciesReference species = "CLung" stoichiometry = "1"/>
  94             </listOfReactants>
  95             <listOfProducts>
  96                <speciesReference species = "CArt" stoichiometry = "1"/>
  97             </listOfProducts>
  98             <kineticLaw>
  99                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 100                   <apply>
 101                      <divide/>
 102                      <apply>
 103                         <times/>
 104                         <ci>
 105                               QCardiac
 106                         </ci>
 107                         <ci>
 108                               CLung
 109                         </ci>
 110                      </apply>
 111                      <ci>
 112                            VLung
 113                      </ci>
 114                   </apply>
 115                </math>
 116             </kineticLaw>
 117          </reaction>
 118          <reaction id = "J4" reversible = "false">
 119             <listOfReactants>
 120                <speciesReference species = "CVen" stoichiometry = "1"/>
 121             </listOfReactants>
 122             <listOfProducts>
 123                <speciesReference species = "CLung" stoichiometry = "1"/>
 124             </listOfProducts>
 125             <kineticLaw>
 126                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 127                   <apply>
 128                      <divide/>
 129                      <apply>
 130                         <times/>
 131                         <ci>
 132                               QCardiac
 133                         </ci>
 134                         <ci>
 135                               CVen
 136                         </ci>
 137                      </apply>
 138                      <ci>
 139                            VVen
 140                      </ci>
 141                   </apply>
 142                </math>
 143             </kineticLaw>
 144          </reaction>
 145          <reaction id = "J5" reversible = "false">
 146             <listOfReactants>
 147                <speciesReference species = "CArt" stoichiometry = "1"/>
 148             </listOfReactants>
 149             <listOfProducts>
 150                <speciesReference species = "CRest" stoichiometry = "1"/>
 151             </listOfProducts>
 152             <kineticLaw>
 153                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 154                   <apply>
 155                      <divide/>
 156                      <apply>
 157                         <times/>
 158                         <ci>
 159                               QRest
 160                         </ci>
 161                         <ci>
 162                               CArt
 163                         </ci>
 164                      </apply>
 165                      <ci>
 166                            VArt
 167                      </ci>
 168                   </apply>
 169                </math>
 170             </kineticLaw>
 171          </reaction>
 172          <reaction id = "J6" reversible = "false">
 173             <listOfReactants>
 174                <speciesReference species = "CRest" stoichiometry = "1"/>
 175             </listOfReactants>
 176             <listOfProducts>
 177                <speciesReference species = "CVen" stoichiometry = "1"/>
 178             </listOfProducts>
 179             <kineticLaw>
 180                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 181                   <apply>
 182                      <divide/>
 183                      <apply>
 184                         <divide/>
 185                         <apply>
 186                            <divide/>
 187                            <apply>
 188                               <times/>
 189                               <ci>
 190                                     QRest
 191                               </ci>
 192                               <ci>
 193                                     CRest
 194                               </ci>
 195                               <ci>
 196                                     Ratioblood2plasma
 197                               </ci>
 198                            </apply>
 199                            <ci>
 200                                  KRest2plasma
 201                            </ci>
 202                         </apply>
 203                         <ci>
 204                               Fraction_unbound_plasma
 205                         </ci>
 206                      </apply>
 207                      <ci>
 208                            VRest
 209                      </ci>
 210                   </apply>
 211                </math>
 212             </kineticLaw>
 213          </reaction>
 214          <reaction id = "J7" reversible = "false">
 215             <listOfReactants>
 216                <speciesReference species = "CArt" stoichiometry = "1"/>
 217             </listOfReactants>
 218             <listOfProducts>
 219                <speciesReference species = "CLiver" stoichiometry = "1"/>
 220             </listOfProducts>
 221             <kineticLaw>
 222                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 223                   <apply>
 224                      <divide/>
 225                      <apply>
 226                         <times/>
 227                         <ci>
 228                               QLiver
 229                         </ci>
 230                         <ci>
 231                               CArt
 232                         </ci>
 233                      </apply>
 234                      <ci>
 235                            VArt
 236                      </ci>
 237                   </apply>
 238                </math>
 239             </kineticLaw>
 240          </reaction>
 241          <reaction id = "J8" reversible = "false">
 242             <listOfReactants>
 243                <speciesReference species = "CLiver" stoichiometry = "1"/>
 244             </listOfReactants>
 245             <listOfProducts>
 246                <speciesReference species = "CMetabolized" stoichiometry = "1"/>
 247             </listOfProducts>
 248             <kineticLaw>
 249                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 250                   <apply>
 251                      <divide/>
 252                      <apply>
 253                         <divide/>
 254                         <apply>
 255                            <divide/>
 256                            <apply>
 257                               <times/>
 258                               <ci>
 259                                     CLmetabolism
 260                               </ci>
 261                               <ci>
 262                                     CLiver
 263                               </ci>
 264                            </apply>
 265                            <ci>
 266                                  Kliver2plasma
 267                            </ci>
 268                         </apply>
 269                         <ci>
 270                               Fraction_unbound_plasma
 271                         </ci>
 272                      </apply>
 273                      <ci>
 274                            VLiver
 275                      </ci>
 276                   </apply>
 277                </math>
 278             </kineticLaw>
 279          </reaction>
 280          <reaction id = "J9" reversible = "false">
 281             <listOfReactants>
 282                <speciesReference species = "CGut" stoichiometry = "1"/>
 283             </listOfReactants>
 284             <listOfProducts>
 285                <speciesReference species = "CLiver" stoichiometry = "1"/>
 286             </listOfProducts>
 287             <kineticLaw>
 288                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 289                   <apply>
 290                      <divide/>
 291                      <apply>
 292                         <times/>
 293                         <ci>
 294                               QGut
 295                         </ci>
 296                         <ci>
 297                               CGut
 298                         </ci>
 299                      </apply>
 300                      <ci>
 301                            VGut
 302                      </ci>
 303                   </apply>
 304                </math>
 305             </kineticLaw>
 306          </reaction>
 307          <reaction id = "J10" reversible = "false">
 308             <listOfReactants>
 309                <speciesReference species = "CLiver" stoichiometry = "1"/>
 310             </listOfReactants>
 311             <listOfProducts>
 312                <speciesReference species = "CVen" stoichiometry = "1"/>
 313             </listOfProducts>
 314             <kineticLaw>
 315                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 316                   <apply>
 317                      <divide/>
 318                      <apply>
 319                         <divide/>
 320                         <apply>
 321                            <divide/>
 322                            <apply>
 323                               <times/>
 324                               <apply>
 325                                  <plus/>
 326                                  <ci>
 327                                        QLiver
 328                                  </ci>
 329                                  <ci>
 330                                        QGut
 331                                  </ci>
 332                               </apply>
 333                               <ci>
 334                                     CLiver
 335                               </ci>
 336                               <ci>
 337                                     Ratioblood2plasma
 338                               </ci>
 339                            </apply>
 340                            <ci>
 341                                  Kliver2plasma
 342                            </ci>
 343                         </apply>
 344                         <ci>
 345                               Fraction_unbound_plasma
 346                         </ci>
 347                      </apply>
 348                      <ci>
 349                            VLiver
 350                      </ci>
 351                   </apply>
 352                </math>
 353             </kineticLaw>
 354          </reaction>
 355          <reaction id = "J11" reversible = "false">
 356             <listOfReactants>
 357                <speciesReference species = "CArt" stoichiometry = "1"/>
 358             </listOfReactants>
 359             <listOfProducts>
 360                <speciesReference species = "CKidney" stoichiometry = "1"/>
 361             </listOfProducts>
 362             <kineticLaw>
 363                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 364                   <apply>
 365                      <divide/>
 366                      <apply>
 367                         <times/>
 368                         <ci>
 369                               QKidney
 370                         </ci>
 371                         <ci>
 372                               CArt
 373                         </ci>
 374                      </apply>
 375                      <ci>
 376                            VArt
 377                      </ci>
 378                   </apply>
 379                </math>
 380             </kineticLaw>
 381          </reaction>
 382          <reaction id = "J12" reversible = "false">
 383             <listOfReactants>
 384                <speciesReference species = "CKidney" stoichiometry = "1"/>
 385             </listOfReactants>
 386             <listOfProducts>
 387                <speciesReference species = "CTubules" stoichiometry = "1"/>
 388             </listOfProducts>
 389             <kineticLaw>
 390                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 391                   <apply>
 392                      <divide/>
 393                      <apply>
 394                         <divide/>
 395                         <apply>
 396                            <times/>
 397                            <ci>
 398                                  Qgfr
 399                            </ci>
 400                            <ci>
 401                                  CKidney
 402                            </ci>
 403                         </apply>
 404                         <ci>
 405                               Kkidney2plasma
 406                         </ci>
 407                      </apply>
 408                      <ci>
 409                            VKidney
 410                      </ci>
 411                   </apply>
 412                </math>
 413             </kineticLaw>
 414          </reaction>
 415          <reaction id = "J13" reversible = "false">
 416             <listOfReactants>
 417                <speciesReference species = "CKidney" stoichiometry = "1"/>
 418             </listOfReactants>
 419             <listOfProducts>
 420                <speciesReference species = "CVen" stoichiometry = "1"/>
 421             </listOfProducts>
 422             <kineticLaw>
 423                <math xmlns = "http://www.w3.org/1998/Math/MathML">
 424                   <apply>
 425                      <divide/>
 426                      <apply>
 427                         <divide/>
 428                         <apply>
 429                            <divide/>
 430                            <apply>
 431                               <times/>
 432                               <ci>
 433                                     QKidney
 434                               </ci>
 435                               <ci>
 436                                     CKidney
 437                               </ci>
 438                               <ci>
 439                                     Ratioblood2plasma
 440                               </ci>
 441                            </apply>
 442                            <ci>
 443                                  Kkidney2plasma
 444                            </ci>
 445                         </apply>
 446                         <ci>
 447                               Fraction_unbound_plasma
 448                         </ci>
 449                      </apply>
 450                      <ci>
 451                            VKidney
 452                      </ci>
 453                   </apply>
 454                </math>
 455             </kineticLaw>
 456          </reaction>
 457       </listOfReactions>
 458    </model>
 459 </sbml>

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