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BIOMD0000000197 - Bartholome2007_MDCKII

 

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Reference Publication
Publication ID: 17548463
Bartholomé K, Rius M, Letschert K, Keller D, Timmer J, Keppler D.
Data-based mathematical modeling of vectorial transport across double-transfected polarized cells.
Drug Metab. Dispos. 2007 Sep; 35(9): 1476-1481
Institute for Physics, University of Freiburg, Freiburg, Germany.  [more]
Model
Original Model: BIOMD0000000197.origin
Submitter: Kilian Bartholomé
Submission ID: MODEL0212154960
Submission Date: 22 Oct 2008 15:50:59 UTC
Last Modification Date: 07 Apr 2014 00:50:13 UTC
Creation Date: 25 Sep 2008 16:51:05 UTC
Encoders:  Kilian Bartholomé
   Lukas Endler
set #1
bqbiol:isVersionOf Gene Ontology regulation of cellular localization
bqbiol:hasTaxon Taxonomy Mammalia
Notes

SBML model exported from PottersWheel on 2007-09-19 15:35:47.

The values for parameters and the inital concentrations of this model where directly provided by the main author:

Parameter values
parameter value unit
p1 0.0025 1/min
p2 0.0784 1/min
p3 0.0013 1/min
p4 0.0827 1/min
p5 0.0091 1/min
p6 0.000064 1/(nmole*min)
p7 0.0397 1/min
p8 1000 nmole
p9 0.0098 1/(nmole*min)
p10 1.6 1/min
p11 1000 nmole
p12 0.0003 ml/min
The basal chamber volume was taken as 1 ml, the apical as 1.5. As starting values x1 was set to 88 nmole, all other species to 0.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 17548463 Submission Date: 22 Oct 2008 15:50:59 UTC Last Modification Date: 07 Apr 2014 00:50:13 UTC Creation Date: 25 Sep 2008 16:51:05 UTC
Mathematical expressions
Reactions
OATP1B3 mediated import ABCC2 mediated export endogenous basolateral import endogenous basolateral export
endogenous apical export basolateral BSP binding basolateral BSP dissoc cellular BSP binding
cellular BSP dissoc paracellular transport    
Rules
Assignment Rule (variable: total BSP) Assignment Rule (variable: intracellular BSP)    
Physical entities
Compartments Species
basolateral extrocellular space free basolateral BSP basolateral bound BSP  
intracellular free intracellular BSP bound intracellular BSP intracellular BSP
apical extracellular space apical BSP total BSP  
Global parameters
p1 p2 p3 p4
p5 p6 p7 p8
p9 p10 p11 p12
Reactions (10)
 
 OATP1B3 mediated import [free basolateral BSP] → [free intracellular BSP];  
 
 ABCC2 mediated export [free intracellular BSP] → [apical BSP];  
 
 endogenous basolateral import [free basolateral BSP] → [free intracellular BSP];  
 
 endogenous basolateral export [free intracellular BSP] → [free basolateral BSP];  
 
 endogenous apical export [free intracellular BSP] → [apical BSP];  
 
 basolateral BSP binding [free basolateral BSP] → [basolateral bound BSP];  
 
 basolateral BSP dissoc [basolateral bound BSP] → [free basolateral BSP];  
 
 cellular BSP binding [free intracellular BSP] → [bound intracellular BSP];  
 
 cellular BSP dissoc [bound intracellular BSP] → [free intracellular BSP];  
 
 paracellular transport [free basolateral BSP] ↔ [apical BSP];  
 
Rules (2)
 
 Assignment Rule (name: BSP_tot) total BSP = x1+x2+x3+x4+x5
 
 Assignment Rule (name: BSP_cell) intracellular BSP = x3+x4
 
 basolateral extrocellular space Spatial dimensions: 3.0  Compartment size: 1.0
 
 free basolateral BSP
Compartment: basolateral extrocellular space
Initial amount: 88.0
 
 basolateral bound BSP
Compartment: basolateral extrocellular space
Initial amount: 0.0
 
 intracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 free intracellular BSP
Compartment: intracellular
Initial amount: 0.0
 
 bound intracellular BSP
Compartment: intracellular
Initial amount: 0.0
 
  intracellular BSP
Compartment: intracellular
 
 apical extracellular space Spatial dimensions: 3.0  Compartment size: 1.5
 
 apical BSP
Compartment: apical extracellular space
Initial amount: 0.0
 
  total BSP
Compartment: apical extracellular space
 
Global Parameters (12)
 
   p1
Value: 0.0025   (Units: permin)
Constant
 
   p2
Value: 0.0784   (Units: permin)
Constant
 
   p3
Value: 0.0013   (Units: permin)
Constant
 
   p4
Value: 0.0827   (Units: permin)
Constant
 
   p5
Value: 0.0091   (Units: permin)
Constant
 
   p6
Value: 6.4E-5   (Units: per_nmole_per_ml)
Constant
 
   p7
Value: 0.0397   (Units: permin)
Constant
 
   p8
Value: 1000.0   (Units: nmole)
Constant
 
   p9
Value: 0.0098   (Units: per_nmole_per_ml)
Constant
 
   p10
Value: 1.6   (Units: permin)
Constant
 
   p11
Value: 1000.0   (Units: nmole)
Constant
 
   p12
Value: 3.0E-4   (Units: ml_per_min)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000197

Curator's comment: (updated: 22 Oct 2008 16:50:42 BST)

Reproduction of the time courses in figure 3 of the original publication.
The simulation was run using SBML odeSolver and plotted using xmgrace

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