band1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000413) Biomodels notes: Figure s15 in the supplementary material of the reference publication has been reproduced here. Figure E in the curation figure also corresponds to Figure 2A of the reference publication. The model as such corresponds to the auxin dose of 10nM (cyan line in the plot). Different auxin doses are incorporated in the model using the parameter, alpha_tr. alpha_tr = 5.83 (no auxin) alpha_tr = 7.44 (1nM) alpha_tr = 19.96 (5nM) alpha_tr = 30.50 (10nM) alpha_tr = 132.82 (100nM) alpha_tr = 270.52 (1000nM). The model was simulated using Copasi v4.8 (Build 35). JWS Online curation: This model was curated by reproducing the Figure S15A.
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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 | |
|---|---|---|---|---|---|
| TIR1 | — | 15.4 | cell | ✘ | |
| VENUS | — | 40.4 | cell | ✘ | |
| auxin | — | 7.38 | cell | ✘ | |
| auxinTIR1 | — | 0.28 | cell | ✘ | |
| auxinTIR1VENUS | — | 2.78 | 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 | |
|---|---|---|---|---|---|
| VENUSphotobleachingdecay | — | VENUS > ∅ lambda * VENUS | |||
| VENUSproduction | — | ∅ > VENUS delta | |||
| auxin_TIR1_VENUSassociation | — | auxinTIR1 + VENUS > auxinTIR1VENUS la * auxinTIR1 * VENUS | |||
| auxin_TIR1_VENUSdissociation | — | auxinTIR1VENUS > auxinTIR1 + VENUS ld * auxinTIR1VENUS | |||
| auxin_TIR1_VENUSdissociationleadingtoubiquitination | — | auxinTIR1VENUS > auxinTIR1 lm * auxinTIR1VENUS | |||
| auxin_TIR1association | — | auxin + TIR1 > auxinTIR1 ka * auxin * TIR1 | |||
| auxin_TIR1dissociation | — | auxinTIR1 > auxin + TIR1 kd * auxinTIR1 | |||
| auxindecay | — | auxin > ∅ mu * auxin | |||
| auxinproduction | — | ∅ > auxin alpha_tr |
| Id | Value | |
|---|---|---|
| TIR1T | 18.5 | |
| alpha_tr | 30.5 | |
| delta | 0.486 | |
| ka | 0.000822 | |
| kd | 0.334 | |
| la | 1.15 | |
| lambda | 0.00316 | |
| ld | 4.49 | |
| lm | 0.175 | |
| mu | 0.79 |
| Id | Value | Reaction |
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| Trigger | Assignments |
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