bartholome1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000197) Biomodels notes: 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. Reproduction of the time courses in figure 3 of the original publication. The simulation was run using SBML odeSolver and plotted using xmgrace. JWS Online curation: Curves x5 and x3 + x4 OATP1B3-ABCC2 of Figure 3 were recreated.
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Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.
| Name | Definition | |
|---|---|---|
| — | 1e-09 mole | |
| — | 0.001 litre | |
| — | 60.0 second | |
| — | 0.016666666666666666 second^(-1.0) | |
| — | 1.6666666666666667e-05 litre second^(-1.0) | |
| — | 16666666.666666666 mole^(-1.0) second^(-1.0) |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| apical | apical extracellular space | 3.0 | 1.5 | |
| basolat | basolateral extrocellular space | 3.0 | 1.0 | |
| cell | intracellular | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| BSP_cell | intracellular BSP | 0.0 | cell (intracellular) | ✔ | |
| BSP_tot | total BSP | 0.0 | apical (apical extracellular space) | ✔ | |
| x1 | free basolateral BSP | 88.0 | basolat (basolateral extrocellular space) | ✘ | |
| x2 | basolateral bound BSP | 0.0 | basolat (basolateral extrocellular space) | ✘ | |
| x3 | free intracellular BSP | 0.0 | cell (intracellular) | ✘ | |
| x4 | bound intracellular BSP | 0.0 | cell (intracellular) | ✘ | |
| x5 | apical BSP | 0.0 | apical (apical extracellular space) | ✘ |
Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.
| Definition |
|---|
| Id | Name | Objective coefficient | Reaction Equation and Kinetic Law | Flux bounds | |
|---|---|---|---|---|---|
| ABCC2 | ABCC2 mediated export | x3 > x5 p2 * x3 | |||
| OATP1B3 | OATP1B3 mediated import | x1 > x3 p1 * x1 | |||
| bl_BSP_binding | basolateral BSP binding | x1 > x2 p6 * x1 * (p8 - x2) | |||
| bl_BSP_dissoc | basolateral BSP dissoc | x2 > x1 p7 * x2 | |||
| cellular_BSP_binding | cellular BSP binding | x3 > x4 p9 * x3 * (p11 - x4) | |||
| cellular_BSP_dissoc | cellular BSP dissoc | x4 > x3 p10 * x4 | |||
| endo_ex_ap | endogenous apical export | x3 > x5 p5 * x3 | |||
| endo_ex_bl | endogenous basolateral export | x3 > x1 p4 * x3 | |||
| endo_in_bl | endogenous basolateral import | x1 > x3 p3 * x1 | |||
| paracell_transp | paracellular transport | x1 = x5 p12 * (x1 / basolat - x5 / apical) |
| Id | Value | |
|---|---|---|
| p1 | 0.0025 permin | |
| p10 | 1.6 permin | |
| p11 | 1000.0 | |
| p12 | 0.0003 ml_per_min | |
| p2 | 0.0784 permin | |
| p3 | 0.0013 permin | |
| p4 | 0.0827 permin | |
| p5 | 0.0091 permin | |
| p6 | 6.4e-05 per_nmole_per_ml | |
| p7 | 0.0397 permin | |
| p8 | 1000.0 | |
| p9 | 0.0098 per_nmole_per_ml |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| BSP_cell = x3 + x4 | |
| BSP_tot = x1 + x2 + x3 + x4 + x5 |
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| Trigger | Assignments |
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