Warning! Found 2 non-fixable id collusion: task1_model1_machado1_time, task2_model2_machado1_time
Info! Removed 11 unused DataGenerator from this document

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

A model of cell cycle behavior dominated by kinetics of a pathway stimulated by growth factors.

  • MN Obeyesekere
  • SO Zimmerman
  • ES Tecarro
  • G Auchmuty
Bull. Math. Biol. 1999; 61 (5): 917-934
Abstract
A modified version of a previously developed mathematical model [Obeyesekere et al., Cell Prolif. (1997)] of the G1-phase of the cell cycle is presented. This model describes the regulation of the G1-phase that includes the interactions of the nuclear proteins, RB, cyclin E, cyclin D, cdk2, cdk4 and E2F. The effects of the growth factors on cyclin D synthesis under saturated or unsaturated growth factor conditions are investigated based on this model. The solutions to this model (a system of nonlinear ordinary differential equations) are discussed with respect to existing experiments. Predictions based on mathematical analysis of this model are presented. In particular, results are presented on the existence of two stable solutions, i.e., bistability within the G1-phase. It is shown that this bistability exists under unsaturated growth factor concentration levels. This phenomenon is very noticeable if the efficiency of the signal transduction, initiated by the growth factors leading to cyclin D synthesis, is low. The biological significance of this result as well as possible experimental designs to test these predictions are presented.

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)

Global parameters

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

Local parameters

Id Value Reaction

Assignment rules

Definition
RP_1 = RT_1 - RS_1 - R_1
E2F_1 = theta_1 - RS_1
unpho_RB = R_1 + RS_1

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments