metaid_0000036
constant: true
value: 0.0
type: Parameter

698283
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000026
constant: true
value: 100.0
type: Parameter

698150
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000065
notes: Free CDK ( normalized with c0 )c=(c0-x-x1-ix-ixp)/c0.

metaid_0000046
constant: true
value: 0.1
type: Parameter

metaid_0000056
kinetic law: 698138
modifier: 698126
product: 698114
reactant: 698102
is version of: GO:0006468
fast: false
reversible: true
name: z0 phosphorylation
type: Reaction

metaid_0000075
kinetic law: 698559
product: 698547
reactant: 698535
is version of: GO:0043624
fast: false
reversible: false
name: Cyclin:CDK:CKIp degradation
type: Reaction

698487
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000035
constant: true
value: 50.0
type: Parameter

698619
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000005
initial amount: NaN
name: Inactive Cyclin:CDK complex
in compartment: metaid_0000003
constant: false
has part: IPR006670
type: Species
boundary condition: false
initial concentration: 0.1
has part: GO:0000307
has only substance units: false

metaid_0000025
constant: true
value: 10.0
type: Parameter

698415
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000010
has version: P04821
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: Unphosphorylated CDC25
type: Species

metaid_0000045
constant: true
value: 0.1
type: Parameter

metaid_0000055
kinetic law: 698090
modifier: 698078
reactant: 698066
is version of: GO:0008054
fast: false
reversible: false
name: Cyclin degradation
type: Reaction

metaid_0000076
kinetic law: 698583
reactant: 698571
is version of: GO:0030163
fast: false
reversible: false
name: unphosphorylated wee1 degradation
type: Reaction

metaid_0000039
constant: true
value: 4.0
type: Parameter

698643
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000019
constant: true
value: 300.0
type: Parameter

698162
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000050
is version of: IPR006670
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: Free cyclin
type: Species

metaid_0000083
unit: 697969
name: arbitrary subst.
type: SBMLUnitsDef

metaid_0000024
constant: true
value: 1.0
type: Parameter

metaid_0000070
is version of: IPR006670
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
type: Species

698451
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

698295
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000044
constant: true
value: 0.1
type: Parameter

metaid_0000077
kinetic law: 698607
reactant: 698595
is version of: GO:0030163
fast: false
reversible: false
name: phosphorylated wee1 degradation
type: Reaction

metaid_0000063
name: CKI binding to Active Cyclin:CDK complex
is version of: GO:0032403
product: 698415
is version of: GO:0004861
reactant: 698391
reversible: true
kinetic law: 698427
type: Reaction
fast: false
reactant: 698403

metaid_0000030
constant: true
value: 0.0
type: Parameter

metaid_0000058
kinetic law: 698247
modifier: 698235
product: 698223
reactant: 698210
is version of: GO:0006468
fast: false
reversible: true
name: z1 phosphorylation
type: Reaction

698547
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

698715
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000037
constant: true
value: 25.0
type: Parameter

metaid_0000023
constant: true
value: 0.1
type: Parameter

698066
stoichiometry: 1.0
species: metaid_0000050
type: SpeciesReference

698571
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000084
unit: 697981
name: arbitrary vol
type: SBMLUnitsDef

metaid_0000003
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell
type: Compartment

698367
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000078
kinetic law: 698631
reactant: 698619
is version of: GO:0030163
fast: false
reversible: false
name: Unphosphorylated CDC25 degradation
type: Reaction

metaid_0000064
type: Reaction
product: 698451
is version of: GO:0006468
is version of: GO:0004693
fast: false
reactant: 698439
kinetic law: 698475
name: ix phosphorylation
modifier: 698463
reversible: true

698017
stoichiometry: 1.0
species: metaid_0000050
type: SpeciesReference

698511
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000057
name: x phosphorylation
is version of: GO:0045736
kinetic law: 698198
modifier: 698186
product: 698162
type: Reaction
modifier: 698174
reversible: true
reactant: 698150
fast: false

metaid_0000043
constant: true
value: 10.0
type: Parameter

metaid_0000042
constant: true
value: 10.0
type: Parameter

metaid_0000032
constant: true
value: 1.0
type: Parameter

metaid_0000022
constant: true
value: 30.0
type: Parameter

698403
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000079
kinetic law: 698655
reactant: 698643
is version of: GO:0030163
fast: false
reversible: false
name: One site phosphorylated CDC25 degradaton
type: Reaction

metaid_0000052
is version of: GO:0030332
product: 698029
kinetic law: 698054
type: Reaction
reactant: 698017
fast: false
reversible: true
name: Cyclin binding with CDK
modifier: 698042
is version of: GO:0005515

698029
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

metaid_0000082
kinetic law: 698739
modifier: 698727
reactant: 698715
is version of: GO:0030163
fast: false
reversible: false
name: Active cyclin:CDK complex degradation
type: Reaction

metaid_0000071
notes: Total cyclin (x+x1+y)

metaid_0000013
is homolog to: P30291
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: Unphosphorylated wee1
type: Species

metaid_0000017
initial amount: NaN
constant: false
has part: IPR003175
has part: GO:0000307
type: Species
initial concentration: 0.0
name: Cyclin:CDK:CKI complex with CKI unphosphorylated
has part: IPR006670
has only substance units: false
boundary condition: false
in compartment: metaid_0000003

697993
stoichiometry: 1.0
species: metaid_0000050
type: SpeciesReference

metaid_0000027
constant: true
value: 1.0
type: Parameter

metaid_0000061
kinetic law: 698355
modifier: 698343
product: 698331
is version of: GO:0051488
is version of: GO:0044249
fast: false
reversible: false
name: SKP2 synthesis
type: Reaction

698102
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000041
constant: true
value: 10.0
type: Parameter

698439
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000031
constant: true
value: 1.0
type: Parameter

metaid_0000021
constant: true
value: 30.0
type: Parameter

698391
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000051
kinetic law: 698005
product: 697993
is version of: GO:0044249
fast: false
reversible: false
name: Free cyclin synthesis
type: Reaction

698331
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000081
kinetic law: 698703
product: 698691
is version of: GO:0044249
fast: false
reversible: false
name: Unphosphorylation CDC25 synthesis
type: Reaction

metaid_0000072
constant: true
value: 25.0
type: Parameter

698691
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000059
kinetic law: 698271
product: 698259
is version of: GO:0044249
fast: false
reversible: false
name: unphosphorylated wee1 synthesis
type: Reaction

metaid_0000018
has part: GO:0000307
boundary condition: false
type: Species
in compartment: metaid_0000003
has part: IPR006670
name: Cyclin:CDK:CKI complex with CKI phosphorylated
has only substance units: false
has part: IPR003175
initial concentration: 0.0
initial amount: NaN
constant: false

metaid_0000014
is homolog to: P30291
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: phosphorylated wee1
type: Species

metaid_0000049
constant: true
value: 1.0
type: Parameter

metaid_0000009
is version of: GO:0000307
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: Free CDK
type: Species

metaid_0000062
kinetic law: 698379
product: 698367
is version of: GO:0044249
fast: false
reversible: false
name: CKI synthesis
type: Reaction

metaid_0000028
constant: true
value: 10.0
type: Parameter

698114
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000020
constant: true
value: 5.0
type: Parameter

698223
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000034
constant: true
value: 2.0
type: Parameter

metaid_0000015
initial amount: NaN
constant: false
initial concentration: 0.0
type: Species
is version of: IPR001810
has only substance units: false
name: Active SKP2 or APC
boundary condition: false
is version of: GO:0005680
in compartment: metaid_0000003

metaid_0000011
has version: P04821
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: One-site phosphorylated CDC25
type: Species

metaid_0000073
kinetic law: 698499
reactant: 698487
is version of: GO:0030163
fast: false
reversible: false
name: SKP2 degradation
type: Reaction

metaid_0000080
kinetic law: 698679
reactant: 698667
is version of: GO:0030163
fast: false
reversible: true
name: Two site phosphorylated CDC25 degradation
type: Reaction

698595
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

BIOMD0000000110
reaction: metaid_0000073
parameter: metaid_0000030
parameter: metaid_0000019
reaction: metaid_0000064
parameter: metaid_0000021
time units: metaid_0000276
reaction: metaid_0000057
is described by: http://identifiers.org/pubmed/14645053
reaction: metaid_0000063
species: metaid_0000017
reaction: metaid_0000056
parameter: metaid_0000031
species: metaid_0000012
reaction: metaid_0000077
parameter: metaid_0000034
notes: This model is from the article: Dynamics of the cell cycle: checkpoints, sizers, and timers. Qu Z, MacLellan WR, Weiss JN Biophys. J. 2003 Dec; 85(6): 3600-11 14645053 , Abstract: We have developed a generic mathematical model of a cell cycle signaling network in higher eukaryotes that can be used to simulate both the G1/S and G2/M transitions. In our model, the positive feedback facilitated by CDC25 and wee1 causes bistability in cyclin-dependent kinase activity, whereas the negative feedback facilitated by SKP2 or anaphase-promoting-complex turns this bistable behavior into limit cycle behavior. The cell cycle checkpoint is a Hopf bifurcation point. These behaviors are coordinated by growth and division to maintain normal cell cycle and size homeostasis. This model successfully reproduces sizer, timer, and the restriction point features of the eukaryotic cell cycle, in addition to other experimental findings. Figure6B has been reproduced by both SBMLodeSolver online and MathSBML. We do not include the synthesis of cyclins is proportional to cell size (Equation 2 in Page3604 of the paper) in this model. The author of the paper keep all the variables and parameters dimensionless. But in the model, we choose to use default units of SBML. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
parameter: metaid_0000026
species: metaid_0000070
parameter: metaid_0000028
is version of: GO:0000075
parameter: metaid_0000025
species: metaid_0000007
has version: REACT 152
is version of: GO:0007346
parameter: metaid_0000027
reaction: metaid_0000062
volume units: metaid_0000084
parameter: metaid_0000044
rule: metaid_0000071
reaction: metaid_0000061
species: metaid_0000050
parameter: metaid_0000049
parameter: metaid_0000035
reaction: metaid_0000082
reaction: metaid_0000052
reaction: metaid_0000081
parameter: metaid_0000020
species: metaid_0000018
length unit: length
parameter: metaid_0000072
reaction: metaid_0000076
species: metaid_0000013
reaction: metaid_0000055
species: metaid_0000015
parameter: metaid_0000033
species: metaid_0000008
parameter: metaid_0000043
species: metaid_0000010
rule: metaid_0000065
reaction: metaid_0000079
units def: metaid_0000084
parameter: metaid_0000024
type: SBMLModel
parameter: metaid_0000023
species: metaid_0000005
reaction: metaid_0000074
reaction: metaid_0000060
substance units: metaid_0000083
parameter: metaid_0000048
curated: true
parameter: metaid_0000042
reaction: metaid_0000051
occurs in: http://identifiers.org/taxonomy/2759
parameter: metaid_0000047
reaction: metaid_0000080
reaction: metaid_0000058
parameter: metaid_0000041
species: metaid_0000014
parameter: metaid_0000022
reaction: metaid_0000075
parameter: metaid_0000032
species: metaid_0000016
reaction: metaid_0000078
area units: metaid_0000005
has version: sce04111
species: metaid_0000009
parameter: metaid_0000029
species: metaid_0000011
parameter: metaid_0000046
units def: metaid_0000083

697981
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

metaid_0000029
constant: true
value: 1.0
type: Parameter

697969
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

698667
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000008
is version of: GO:0000307
constant: false
boundary condition: false
has only substance units: false
initial concentration: 200.0
initial amount: NaN
in compartment: metaid_0000003
name: Total CDK
type: Species

metaid_0000048
constant: true
value: 1.0
type: Parameter

metaid_0000007
constant: false
type: Species
has part: IPR006670
in compartment: metaid_0000003
has part: GO:0000307
initial concentration: 0.1
boundary condition: false
initial amount: NaN
has only substance units: false
name: Active Cyclin:CDK complex

698535
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

metaid_0000033
constant: true
value: 1.0
type: Parameter

698210
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000074
kinetic law: 698523
reactant: 698511
is version of: GO:0030163
fast: false
reversible: false
name: CKI degradation
type: Reaction

metaid_0000012
has version: P04821
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: Two-site phosphorylated CDC25
type: Species

metaid_0000016
is version of: IPR003175
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: Free CKI
type: Species

698259
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000047
constant: true
value: 1.0
type: Parameter

metaid_0000060
kinetic law: 698319
modifier: 698307
product: 698295
reactant: 698283
is version of: GO:0006468
fast: false
reversible: true
name: wee1 phosphorylation
type: Reaction

ORG:
  orgname: EMBL-EBI
n:
  given: Lukas
  family: Endler

ORG:
  orgname: BNMC
n:
  given: Enuo
  family: He

W3 CDTF: Mon Sep 29 14:00:19 BST 2008

W3 CDTF: Wed May 16 11:13:14 BST 2012