obeyesekere1
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000168). Biomodels notes: "The model reproduces the time profiles of the different species depicted in Fig 3a of the paper. Model successfully reproduced using MathSBML." JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. In order to reproduce Figure 3A the following initials values (as the manuscript states) were used: D[0] = 0.1, E[0] = 0.6, R[0] = 0.5, RS[0] = 1.0, X[0] = 0.7
None
None
None
None
None
None
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_1 | cell | 3.0 | 1.0 |
| Id | Name | Initial quantity | Compartment | Fixed | |
|---|---|---|---|---|---|
| D_1 | D | 0.1 | cell_1 (cell) | ✘ | |
| E2F_1 | E2F | 0.0 | cell_1 (cell) | ✘ | |
| E_1 | E | 0.6 | cell_1 (cell) | ✘ | |
| RP_1 | RP | 0.0 | cell_1 (cell) | ✘ | |
| RS_1 | RS | 1.0 | cell_1 (cell) | ✘ | |
| R_1 | R | 0.5 | cell_1 (cell) | ✘ | |
| X_1 | X | 0.7 | cell_1 (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 | |
|---|---|---|---|---|---|
| _1 | cycD/CDK4 synthesis | ∅ > D_1 aD_1 * (k_1 * GF_1 / (1 + k_1 * GF_1)) | |||
| _7 | pRB/E2F complex deassociation via cycE/CDK2 | RS_1 > ∅ pE_1 * RS_1 * E_1 / (qE_1 + RS_1 + E_1) | |||
| cycECDK2degradation_1 | cycE/CDK2 degradation | E_1 > ∅ dE_1 * X_1 * E_1 | |||
| cyclebreak_1 | cycle break | X_1 > ∅ dX_1 * X_1 | |||
| cycleprogression_1 | cycle progression | ∅ > X_1 aX_1 * E_1 + f_1 * E2F_1 + g_1 * pow(X_1, 2) * E_1 | |||
| cyclinCDK4degradation_1 | cycD/CDK4 degradation | D_1 > ∅ dD_1 * E_1 * D_1 | |||
| cyclin_1 | cycE/CDK2 synthesis | ∅ > E_1 aE_1 * (1 + af_1 * E2F_1) | |||
| pRBE2Fcomplexassociation_1 | pRB/E2F complex association | R_1 > RS_1 pS_1 * E2F_1 * R_1 | |||
| pRBE2FcomplexdeassociationviacycDCDK4_1 | pRB/E2F complex deassociation via cycD/CDK4 | RS_1 > ∅ pD_1 * RS_1 * D_1 / (qD_1 + RS_1 + D_1) | |||
| pRBpdephosphorylation_1 | pRB-p dephosphorilation | ∅ > R_1 pX_1 * RP_1 * X_1 / (qX_1 + RP_1 + X_1) |
| Id | Value | |
|---|---|---|
| GF_1 | 6.3 | |
| RT_1 | 2.5 | |
| aD_1 | 0.4 | |
| aE_1 | 0.16 | |
| aX_1 | 0.08 | |
| af_1 | 0.9 | |
| dD_1 | 0.4 | |
| dE_1 | 0.2 | |
| dX_1 | 1.04 | |
| f_1 | 0.2 | |
| g_1 | 0.528 | |
| k_1 | 0.05 | |
| pD_1 | 0.48 | |
| pE_1 | 0.096 | |
| pS_1 | 0.6 | |
| pX_1 | 0.48 | |
| qD_1 | 0.6 | |
| qE_1 | 0.6 | |
| qX_1 | 0.8 | |
| theta_1 | 1.5 | |
| unpho_RB | 0.0 |
| Id | Value | Reaction |
|---|
| Definition | |
|---|---|
| RP_1 = RT_1 - RS_1 - R_1 | |
| E2F_1 = theta_1 - RS_1 | |
| unpho_RB = R_1 + RS_1 |
| Definition |
|---|
| Definition |
|---|
| Definition |
|---|
| Trigger | Assignments |
|---|