dupont2
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000113). Biomodels notes: Model reproduces Fig 4 of the paper. For fraction of phosphorylated protein, W_star, the model reproduces panel b in the same figure. Model successfully tested on MathSBML and Jarnac. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. Figure 4C can only be recreated when K1 = K2 = 1 and not K1 = K2 = 10 as is shown in the paper.
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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-06 mole | |
| — | 60.0 second |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cytosol | cytosol | 3.0 | 1.0 | |
| store | store | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| W_star | Phosphorylated protein | 0.0 | cytosol (cytosol) | ✘ | |
| Wt | Total Protein | 1.0 | cytosol (cytosol) | ✘ | |
| Y | — | 1.6 | store (store) | ✘ | |
| Z | — | 0.15 | cytosol (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 | |
|---|---|---|---|---|---|
| Protein_Phosphorylation | Protein Phosphorylation | ∅ = W_star cytosol * (vp / Wt) * (vk / vp * ((1 - W_star) / (K1 + 1 - W_star)) - W_star / (K2 + W_star)) | |||
| R0 | Calcium influx | ∅ > Z cytosol * v0 | |||
| R1 | InsP3 dependent Ca influx | ∅ > Z cytosol * v1_beta | |||
| R2 | ATP driven pumping of Ca into store | Z > Y cytosol * (Vm2 * pow(Z, n) / (pow(Kp, n) + pow(Z, n))) | |||
| R3 | ATP driven pumping into cytosol | Y > Z store * (Vm3 * pow(Y, m) * pow(Z, p) / ((pow(Kr, m) + pow(Y, m)) * (pow(K_A, p) + pow(Z, p)))) | |||
| R_eff | Ca efflux | Z > ∅ cytosol * k * Z | |||
| Rf | Calcium leak | Y > Z store * kf * Y |
| Id | Value | |
|---|---|---|
| K1 | 0.01 | |
| K2 | 0.01 | |
| K_A | 0.9 | |
| Ka | 2.5 | |
| Kp | 1.0 | |
| Kr | 2.0 | |
| Vm2 | 65.0 | |
| Vm3 | 500.0 | |
| k | 10.0 | |
| kf | 1.0 | |
| m | 2.0 | |
| n | 2.0 | |
| p | 4.0 | |
| q | 1.0 | |
| v0 | 1.0 | |
| v1_beta | 2.7 | |
| vMK | 20.0 | |
| vk | 0.0 | |
| vp | 2.5 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| vk = vMK * pow(Z, q) / (pow(Ka, q) + pow(Z, q)) |
| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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