aguda1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000169) Biomodels notes: The plots correspond to the time profiles of p27, E2F and cycE/CDK2 as depicted in Fig 5c of the paper. MathSBML was used to obtain simulation results. 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 | |
|---|---|
| aguda1999_Fig5C |
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 | |
|---|---|---|---|---|
| default_compartment | — | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| CYCDcdk4 | — | 0.0 | default_compartment | ✘ | |
| CYCDcdk4p27 | — | 0.0 | default_compartment | ✘ | |
| CYCEcdk2p27 | — | 1.0 | default_compartment | ✘ | |
| E2F | — | 0.0 | default_compartment | ✘ | |
| aCYCEcdk2 | — | 0.0 | default_compartment | ✘ | |
| aCYCEcdk20 | — | 5.0 | default_compartment | ✘ | |
| aCYCEcdk21 | — | 0.01 | default_compartment | ✘ | |
| iCYCEcdk2 | — | 0.01 | default_compartment | ✘ | |
| p27 | — | 2.0 | default_compartment | ✘ | |
| pRB | — | 0.05 | default_compartment | ✘ | |
| pRBE2F | — | 1.95 | default_compartment | ✘ | |
| xvar | — | 0.0 | default_compartment | ✔ |
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 | |
|---|---|---|---|---|---|
| v_1 | v_1 | pRBE2F = aCYCEcdk21 + E2F k1*aCYCEcdk2*pRBE2F + k1a*CYCDcdk4*pRBE2F + k1aa*CYCDcdk4p27*pRBE2F | |||
| v_10 | — | CYCDcdk4 = xvar kmin6*CYCDcdk4 | |||
| v_11 | — | xvar = p27 k7 | |||
| v_12 | v_12 | p27 = xvar k8*aCYCEcdk2*p27 | |||
| v_13 | — | aCYCEcdk2 + p27 = CYCEcdk2p27 k9*aCYCEcdk2*p27 | |||
| v_14 | — | CYCEcdk2p27 = aCYCEcdk2 + p27 k10*CYCEcdk2p27 | |||
| v_15 | — | aCYCEcdk20 + CYCDcdk4 = xvar k17*aCYCEcdk20*CYCDcdk4 | |||
| v_16 | — | xvar = E2F k18*E2F | |||
| v_17 | — | CYCDcdk4 + p27 = CYCDcdk4p27 k19*CYCDcdk4*p27 | |||
| v_18 | — | CYCDcdk4p27 = CYCDcdk4 + p27 k20*CYCDcdk4p27 | |||
| v_19 | — | aCYCEcdk2 = xvar k21*aCYCEcdk2^2 | |||
| v_2 | — | E2F + pRB = pRBE2F kmin1*E2F*pRB | |||
| v_20 | — | p27 = xvar k22*p27 | |||
| v_21 | — | xvar = aCYCEcdk20 k23 | |||
| v_22 | — | aCYCEcdk20 = xvar k24*aCYCEcdk20 | |||
| v_23 | v_23 | xvar = aCYCEcdk20 k25/(1 + k25a*pRB) | |||
| v_24 | v_24 | xvar = pRB k26/(1 + k26a*aCYCEcdk20) | |||
| v_25 | — | xvar = pRB k27 | |||
| v_26 | — | pRB = xvar k28*pRB | |||
| v_27 | — | aCYCEcdk21 = pRB k29*aCYCEcdk21 | |||
| v_3 | — | iCYCEcdk2 = aCYCEcdk2 k2*aCYCEcdk2*iCYCEcdk2 | |||
| v_4 | — | aCYCEcdk2 = iCYCEcdk2 kmin2*aCYCEcdk2 | |||
| v_5 | v_5 | xvar = iCYCEcdk2 k3a + k3*E2F | |||
| v_6 | — | xvar = E2F k4 | |||
| v_7 | — | E2F = xvar kmin4*E2F | |||
| v_8 | — | iCYCEcdk2 = xvar k5*iCYCEcdk2 | |||
| v_9 | — | xvar = CYCDcdk4 k6 |
| Id | Value | |
|---|---|---|
| k1 | 0.1 | |
| k10 | 0.035 | |
| k17 | 3.5 | |
| k18 | 0.00001 | |
| k19 | 0.05 | |
| k1a | 0.5 | |
| k1aa | 0.5 | |
| k2 | 0.1 | |
| k20 | 0.01 | |
| k21 | 0.1 | |
| k22 | 0.001 | |
| k23 | 0.2 | |
| k24 | 0.1 | |
| k25 | 0.01 | |
| k25a | 0.02 | |
| k26 | 0.01 | |
| k26a | 0.1 | |
| k27 | 0.01 | |
| k28 | 0.01 | |
| k29 | 0.001 | |
| k3 | 1.42 | |
| k3a | 0.0 | |
| k4 | 0.000001 | |
| k5 | 0.02 | |
| k6 | 0.018 | |
| k7 | 0.00001 | |
| k8 | 2.0 | |
| k9 | 2.0 | |
| kmin1 | 0.001 | |
| kmin2 | 1.0 | |
| kmin4 | 0.016 | |
| kmin6 | 5.0 |
| Id | Value | Reaction |
|---|
| Definition |
|---|
| Definition |
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| Definition |
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| Definition |
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| Trigger | Assignments |
|---|