clarke1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000112) Biomodels notes: The model reproduces the temporal evolution of four variables depicted in Fig 2a. The solution is generated for median parameter values as given in Table 3. Result shown was generated by MathSBML. 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 | |
|---|---|
| clarke2006_Fig2 |
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 | |
|---|---|---|
| — | 60.0 second | |
| — | 1.0 item | |
| — | 0.016666666666666666 second^(-1.0) | |
| — | 0.016666666666666666 item second^(-1.0) | |
| — | 0.016666666666666666 item^(-1.0) second^(-1.0) |
| Id | Name | Spatial dimensions | Size | |
|---|---|---|---|---|
| cytoplasm | cytoplasm | 3.0 | 1.0 | |
| nucleus | nucleus | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| Pi | Pi | 0.0 | nucleus (nucleus) | ✘ | |
| R_smad_P_cyt | R-Smad-P_cyt | 0.0 | cytoplasm (cytoplasm) | ✘ | |
| R_smad_P_nuc | R-Smad-P_nuc | 0.0 | nucleus (nucleus) | ✘ | |
| R_smad_P_smad4_cyt | R-Smad-P-Smad4_cyt | 0.0 | cytoplasm (cytoplasm) | ✘ | |
| R_smad_P_smad4_nuc | R-Smad-P-Smad4_nuc | 0.0 | nucleus (nucleus) | ✘ | |
| R_smad_cyt | R-Smad_cyt | 162000.0 | cytoplasm (cytoplasm) | ✘ | |
| R_smad_nuc | R-Smad_nuc | 18000.0 | nucleus (nucleus) | ✘ | |
| receptor | receptors | 10000.0 | cytoplasm (cytoplasm) | ✘ | |
| smad4_cyt | Smad4_cyt | 120000.0 | cytoplasm (cytoplasm) | ✘ | |
| smad4_nuc | Smad4_nuc | 30000.0 | nucleus (nucleus) | ✘ |
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_0 | Receptor degradation | receptor > ∅ 100 * exp(-time / 90) | |||
| reaction_1 | Phosphorylation | R_smad_cyt > R_smad_P_cyt KCAT * receptor * R_smad_cyt / (K1 + R_smad_cyt) | |||
| reaction_2 | Complex formation | R_smad_P_cyt + smad4_cyt = R_smad_P_smad4_cyt k2a * R_smad_P_cyt * smad4_cyt - k2d * R_smad_P_smad4_cyt | |||
| reaction_3 | Complex translocation | R_smad_P_smad4_cyt > R_smad_P_smad4_nuc k3 * R_smad_P_smad4_cyt | |||
| reaction_4 | Smad4 translocation | smad4_nuc = smad4_cyt k4nc * smad4_nuc - k4cn * smad4_cyt | |||
| reaction_5 | R-Smad translocation | R_smad_nuc = R_smad_cyt k5nc * R_smad_nuc - k5cn * R_smad_cyt | |||
| reaction_6 | Complex in nucleus | R_smad_P_smad4_nuc = smad4_nuc + R_smad_P_nuc k6d * R_smad_P_smad4_nuc - k6a * smad4_nuc * R_smad_P_nuc | |||
| reaction_7 | Dephosphorylation | R_smad_P_nuc > R_smad_nuc + Pi Vmax7 * R_smad_P_nuc / (K7 + R_smad_P_nuc) |
| Id | Value | |
|---|---|---|
| sum_R_smad_cyt | 0.0 | |
| sum_R_smad_nuc | 0.0 | |
| sum_smad4_cyt | 0.0 | |
| sum_smad4_nuc | 0.0 |
| Id | Value | Reaction | |
|---|---|---|---|
| KCAT | 3.51 min_inv | reaction_1 (Phosphorylation) | |
| K1 | 289000.0 substance | reaction_1 (Phosphorylation) | |
| k5nc | 5.63 min_inv | reaction_5 (R-Smad translocation) | |
| k5cn | 0.563 min_inv | reaction_5 (R-Smad translocation) | |
| k4nc | 0.783 min_inv | reaction_4 (Smad4 translocation) | |
| k4cn | 0.00497 min_inv | reaction_4 (Smad4 translocation) | |
| k2a | 0.000065 | reaction_2 (Complex formation) | |
| k2d | 0.0399 min_inv | reaction_2 (Complex formation) | |
| k3 | 16.6 min_inv | reaction_3 (Complex translocation) | |
| k6d | 0.0492 min_inv | reaction_6 (Complex in nucleus) | |
| k6a | 0.000144 | reaction_6 (Complex in nucleus) | |
| Vmax7 | 17100.0 items per min | reaction_7 (Dephosphorylation) | |
| K7 | 8950.0 substance | reaction_7 (Dephosphorylation) |
| Definition | |
|---|---|
| sum_smad4_cyt = smad4_cyt + R_smad_P_smad4_cyt | |
| sum_R_smad_cyt = R_smad_cyt + R_smad_P_cyt + R_smad_P_smad4_cyt | |
| sum_smad4_nuc = smad4_nuc + R_smad_P_smad4_nuc | |
| sum_R_smad_nuc = R_smad_nuc + R_smad_P_nuc + R_smad_P_smad4_nuc |
| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
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