clancy1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000121) Biomodels notes: This model is according to the paper Cellular consequences of HEGR mutations in the long QT syndrome: precursors to sudden cardiac death. The author used Markovian model of cardiac Ikr in the paper. Figure4B in the paper has been reproduced using CellDesigner3.5.1. The cell is depolarized to the indicated test potential for 250ms (from 50ms to 300ms) from a holding potential of -40mV and then repolarized to -40mV. Change the value for vtest from -30,-20,-10,0,10,20,30,40 for each simulation in order to produce the different cureve in the paper. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.
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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 |
|---|
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cell | cell | — | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| c1 | — | 0.0 | cell (cell) | ✘ | |
| c2 | — | 0.0 | cell (cell) | ✘ | |
| c3 | — | 1.0 | cell (cell) | ✘ | |
| i | — | 0.0 | cell (cell) | ✘ | |
| o | — | 0.06 | cell (cell) | ✘ |
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 | |
|---|---|---|---|---|---|
| reaction0000001 | — | c3 = c2 cell*(-(b*c2) + a*c3) | |||
| reaction0000002 | — | c2 = c1 cell*(-(bin*c1) + ain*c2) | |||
| reaction0000003 | — | c1 = o cell*(aa*c1 - bb*o) | |||
| reaction0000004 | — | o = i cell*(-(ai*i) + bi*o) | |||
| reaction0000005 | — | c1 = i cell*(aa*c1 - u*i) |
| Id | Value | |
|---|---|---|
| F | 96.485 | |
| Gk | 0.0 | |
| R | 8.314 | |
| Temp | 310.0 | |
| a | 0.0 | |
| aa | 0.0 | |
| ai | 0.0 | |
| ain | 2.172 | |
| b | 0.0 | |
| bb | 0.0 | |
| bi | 0.0 | |
| bin | 1.077 | |
| ik | 0.0 | |
| ki | 140.0 | |
| ko | 5.4 | |
| u | 0.0 | |
| v | -40.0 | |
| vhold | -40.0 | |
| vk | 0.0 | |
| vtest | 0.0 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| aa = 0.0655*exp(0.05547153*(-36.0 + v)) | |
| ik = Gk*(v - vk)*o | |
| a = 0.0555*exp(0.05547153*(-12.0 + v)) | |
| b = 0.002357*exp(-0.036588*v) | |
| Gk = 0.013500000000000002*ko^0.59 | |
| bi = 1.030072027074169*exp(0.000942*v)*(ko^(-1.0))^0.3 | |
| u = (ai*bb)/bi | |
| bb = 0.0029357000000000003*exp(-0.02158*v) | |
| vk = (R*Temp*log(ko/ki))/F | |
| ai = 1.9755*exp(-0.02352*(25.0 + v))/ko | |
| v = piecewise(vtest,50.0<time<=300.0,vhold) |
| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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