dupont1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000117) Biomodels notes: Figure4B in the paper has been reproduced by RoadRunner and MathSBML. Damped Ca2+ oscillations elicited by a transient pulse of InsP3 applied intracellularly to a resting, non-oscillatory cell. 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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| Simulation | |
|---|---|
| dupont1991_Fig4B |
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-06 mole |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| Cytosol | — | 3.0 | 1.0 | |
| extracellular | — | 3.0 | 1.0 | |
| intracellular_Ca_storepool | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| y | Ca in the InsP3-insensitive pool | 1.4 | intracellular_Ca_storepool | ✘ | |
| z | Ca in the cytosol | 0.1 | Cytosol | ✘ |
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 | |
|---|---|---|---|---|---|
| reaction_0000001 | InsP3 modulated release of Ca from the InsP3 sensitive store | ∅ > z v1 * beta * Cytosol | |||
| reaction_0000002 | Constant input of Ca from the extracellular medium | ∅ > z v0 * Cytosol | |||
| reaction_0000003 | Leak Ca from pool to cytosol | y > z kf * y * Cytosol | |||
| reaction_0000004 | Pumping Ca into the InsP3-insensitive store | z > y intracellular_Ca_storepool * VM2 * pow(z, n) / (pow(K2, n) + pow(z, n)) | |||
| reaction_0000005 | Release of Ca from the pool into the cytosol | y > z Cytosol * VM3 * (pow(y, m) / (pow(KR, m) + pow(y, m))) * (pow(z, p) / (pow(KA, p) + pow(z, p))) | |||
| reaction_0000006 | Transport of cytosolic ca into the extracellular medium | z > ∅ k * z * extracellular |
| Id | Value | |
|---|---|---|
| K2 | 1.0 | |
| KA | 0.9 | |
| KR | 2.0 | |
| VM2 | 65.0 | |
| VM3 | 500.0 | |
| beta | 0.0 | |
| flag | 0.0 | |
| k | 10.0 | |
| kf | 1.0 | |
| m | 2.0 | |
| n | 2.0 | |
| p | 4.0 | |
| tstim | 4.0 | |
| v0 | 1.0 | |
| v1 | 7.3 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| beta = flag * 0.96 * exp(-0.2 * (time - tstim)) |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments | |
|---|---|---|
| gt(time, tstim) | flag = 1 |