BioModels Database logo

BioModels Database

spacer

BIOMD0000000207 - Romond1999_CellCycle

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 10415827
Romond PC, Rustici M, Gonze D, Goldbeter A.
Alternating oscillations and chaos in a model of two coupled biochemical oscillators driving successive phases of the cell cycle.
Ann. N. Y. Acad. Sci. 1999 Jun; 879: 180-193
Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium.  [more]
Model
Original Model: BIOMD0000000207.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL1111382868
Submission Date: 27 Nov 2008 20:45:52 UTC
Last Modification Date: 05 Jul 2012 16:48:46 UTC
Creation Date: 10 Sep 2008 13:58:58 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf KEGG Pathway hsa04110
Gene Ontology mitotic cell cycle
bqbiol:occursIn Taxonomy Eukaryota
Notes

The model reproduces Fig 3 of the paper. Model successfully reproduced using MathSBML and Jarnac.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 10415827 Submission Date: 27 Nov 2008 20:45:52 UTC Last Modification Date: 05 Jul 2012 16:48:46 UTC Creation Date: 10 Sep 2008 13:58:58 UTC
Mathematical expressions
Reactions
cdk2 mediated cyclinB synthesis Ubiquitin ligase mediated cyclinB degradation cyclinB degradation cyclinE synthesis
Ubiquitin ligase mediated cyclinE degradation cyclinE degradation    
Rules
Assignment Rule (variable: V1) Assignment Rule (variable: V3) Assignment Rule (variable: U1) Assignment Rule (variable: U3)
Rate Rule (variable: cdk1) Rate Rule (variable: ubiquitin ligase) Rate Rule (variable: cdk2) Rate Rule (variable: Ubiquitin ligase 2)
Physical entities
Compartments Species
compartment cyclinB cdk1 ubiquitin ligase
cyclinE cdk2 Ubiquitin ligase 2
Global parameters
V1 Kc1 V_M1 V3
V_M3 U1 Kc2 U_M1
U3 U_M3 vi1 Kim1
vd1 K_d1 kd1 K1
V2 K2 K3 V4
K4 vi2 Kim2 vd2
K_d2 kd2 H1 U2
H2 H3 U4 H4
Reactions (6)
 
 cdk2 mediated cyclinB synthesis  → [cyclinB];   {cdk2}
 
 Ubiquitin ligase mediated cyclinB degradation [cyclinB] → ;   {ubiquitin ligase}
 
 cyclinB degradation [cyclinB] → ;  
 
 cyclinE synthesis  → [cyclinE];   {cdk1}
 
 Ubiquitin ligase mediated cyclinE degradation [cyclinE] → ;   {Ubiquitin ligase 2}
 
 cyclinE degradation [cyclinE] → ;  
 
Rules (8)
 
 Assignment Rule (name: V1) V1 = C1/(Kc1+C1)*V_M1
 
 Assignment Rule (name: V3) V3 = M1*V_M3
 
 Assignment Rule (name: U1) U1 = C2/(Kc2+C2)*U_M1
 
 Assignment Rule (name: U3) U3 = M2*U_M3
 
 Rate Rule (name: M1) d [ cdk1] / d t= V1*(1-M1)/(K1+(1-M1))-V2*M1/(K2+M1)
 
 Rate Rule (name: X1) d [ ubiquitin ligase] / d t= V3*(1-X1)/(K3+(1-X1))-V4*X1/(K4+X1)
 
 Rate Rule (name: M2) d [ cdk2] / d t= U1*(1-M2)/(H1+(1-M2))-U2*M2/(H2+M2)
 
 Rate Rule (name: X2) d [ Ubiquitin ligase 2] / d t= U3*(1-X2)/(H3+(1-X2))-U4*X2/(H4+X2)
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 cyclinB
Compartment: compartment
Initial concentration: 2.0  (Units: micromole)
 
 cdk1
Compartment: compartment
Initial amount: 1.0  (Units: dimensionless)
 
 ubiquitin ligase
Compartment: compartment
Initial amount: 0.0  (Units: dimensionless)
 
 cyclinE
Compartment: compartment
Initial concentration: 0.0  (Units: micromole)
 
 cdk2
Compartment: compartment
Initial amount: 0.0  (Units: dimensionless)
 
 Ubiquitin ligase 2
Compartment: compartment
Initial amount: 0.0  (Units: dimensionless)
 
Global Parameters (32)
 
   V1  
 
   Kc1
Value: 0.5   (Units: uM)
Constant
 
   V_M1
Value: 0.3   (Units: min_1)
Constant
 
   V3  
 
   V_M3
Value: 0.1   (Units: min_1)
Constant
 
   U1  
 
   Kc2
Value: 0.5   (Units: uM)
Constant
 
   U_M1
Value: 0.3   (Units: min_1)
Constant
 
   U3  
 
   U_M3
Value: 0.1   (Units: min_1)
Constant
 
   vi1
Value: 0.05   (Units: uM_min_1)
Constant
 
   Kim1
Value: 0.03   (Units: dimensionless)
Constant
 
   vd1
Value: 0.025   (Units: uM_min_1)
Constant
 
   K_d1
Value: 0.02   (Units: uM)
Constant
 
   kd1
Value: 0.0010   (Units: min_1)
Constant
 
   K1
Value: 0.01   (Units: dimensionless)
Constant
 
   V2
Value: 0.15   (Units: min_1)
Constant
 
   K2
Value: 0.01   (Units: dimensionless)
Constant
 
   K3
Value: 0.01   (Units: dimensionless)
Constant
 
   V4
Value: 0.05   (Units: min_1)
Constant
 
   K4
Value: 0.01   (Units: dimensionless)
Constant
 
   vi2
Value: 0.05   (Units: uM_min_1)
Constant
 
   Kim2
Value: 0.03   (Units: dimensionless)
Constant
 
   vd2
Value: 0.025   (Units: uM_min_1)
Constant
 
   K_d2
Value: 0.02   (Units: uM)
Constant
 
   kd2
Value: 0.0010   (Units: min_1)
Constant
 
   H1
Value: 0.01   (Units: dimensionless)
Constant
 
   U2
Value: 0.15   (Units: min_1)
Constant
 
   H2
Value: 0.01   (Units: dimensionless)
Constant
 
   H3
Value: 0.01   (Units: dimensionless)
Constant
 
   U4
Value: 0.05   (Units: min_1)
Constant
 
   H4
Value: 0.01   (Units: dimensionless)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000207

Curator's comment: (updated: 27 Nov 2008 20:45:34 GMT)

Plots correspond to cyclins C1, C2 and kinases M1, M2 dynamics as depicted in Fig 3 of the paper. Results obtained using MathSBML.

spacer
spacer