palini1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000325) Biomodels notes: Ligand concentration response curve as in figure 1B of the publication. All calculation were performed using Copasi v4.6.33. Two logarithmic parameter scans over the the given ligand range with steady state determination were combined in the graph. For the low activity state, the systems initial conditions were taken from the steady state values at L = 0.001, for the high activity from L = 0.2. 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 | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| A | — | 0.0 | cell | ✘ | |
| C | — | 0.0 | cell | ✘ | |
| I | — | 1.0 | cell | ✘ | |
| L | — | 0.1 | cell | ✔ | |
| R | — | 1.0 | cell | ✘ | |
| X | — | 0.0 | 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 | |
|---|---|---|---|---|---|
| A_degradation | — | A > ∅ cell * kdegA * A | |||
| C_I_binding | — | C + I = X cell * (k1 * C * I - k2 * X) | |||
| C_degradation | — | C > ∅ cell * kdegC * C | |||
| I_activation | — | X > C + A cell * k3 * X | |||
| I_degradation | — | I > ∅ cell * kdegI * I | |||
| I_expression | — | ∅ > I cell * (BI + TFs * A / (KD + A)) | |||
| R_L_binding | — | R + L = C cell * (kon * L * R - koff * C) | |||
| R_degradation | — | R > ∅ cell * kdegR * R | |||
| R_expression | — | ∅ > R cell * (BR + Rs * A / (KD + A)) | |||
| X_degradation | — | X > ∅ cell * kdegX * X |
| Id | Value | |
|---|---|---|
| BI | 0.005 | |
| BR | 0.005 | |
| KD | 200.0 | |
| Rs | 3.0 | |
| TFs | 3.0 | |
| k1 | 1.0 | |
| k2 | 5.0 | |
| k3 | 45.0 | |
| kdegA | 0.005 | |
| kdegC | 0.01 | |
| kdegI | 0.005 | |
| kdegR | 0.005 | |
| kdegX | 0.005 | |
| koff | 0.05 | |
| kon | 0.001 |
| Id | Value | Reaction |
|---|
| Definition |
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| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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