MODEL1006230004
type: SBMLModel
parameter: 963789
rule: 963730
rule: 963720
parameter: 963777
parameter: 963845
time units: 219790
parameter: 963843
parameter: 963771
parameter: 963781
area units: area
parameter: 963738
parameter: 963818
parameter: 963828
parameter: 963756
parameter: 963744
rule: 963726
parameter: 963820
parameter: 963830
parameter: 963788
parameter: 963798
parameter: 963792
is described by: http://identifiers.org/pubmed/10637314
parameter: 963780
parameter: 963790
parameter: 963805
parameter: 963815
parameter: 963749
parameter: 963757
parameter: 963837
parameter: 963825
parameter: 963775
parameter: 963773
units def: 219694
rule: 963719
parameter: 963795
parameter: 963734
parameter: 963822
parameter: 963812
parameter: 963752
parameter: 963740
parameter: 963750
parameter: 963840
rule: 963714
rule: 963713
rule: 963704
curated: false
substance units: 178797
parameter: 963772
parameter: 963782
notes: This a model from the article: Kinetic analysis of a molecular model of the budding yeast cell cycle. Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. Mol Biol Cell 2000 Jan;11(1):369-91 10637314 , Abstract: The molecular machinery of cell cycle control is known in more detail for budding yeast, Saccharomyces cerevisiae, than for any other eukaryotic organism. In recent years, many elegant experiments on budding yeast have dissected the roles of cyclin molecules (Cln1-3 and Clb1-6) in coordinating the events of DNA synthesis, bud emergence, spindle formation, nuclear division, and cell separation. These experimental clues suggest a mechanism for the principal molecular interactions controlling cyclin synthesis and degradation. Using standard techniques of biochemical kinetics, we convert the mechanism into a set of differential equations, which describe the time courses of three major classes of cyclin-dependent kinase activities. Model in hand, we examine the molecular events controlling "Start" (the commitment step to a new round of chromosome replication, bud formation, and mitosis) and "Finish" (the transition from metaphase to anaphase, when sister chromatids are pulled apart and the bud separates from the mother cell) in wild-type cells and 50 mutants. The model accounts for many details of the physiology, biochemistry, and genetics of cell cycle control in budding yeast. This model was taken from the CellML repository and automatically converted to SBML. The original model was: Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ. (2000) - version=1.0 The original CellML model was created by: Catherine Lloyd c.lloyd@auckland.ac.nz The University of Auckland This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have…
units def: 219657
rule: 963717
parameter: 963739
parameter: 963737
parameter: 963839
parameter: 963767
parameter: 963755
parameter: 963765
parameter: 963833
rule: 963725
parameter: 963821
parameter: 963831
parameter: 963799
rule: 963728
rule: 963711
rule: 963706
parameter: 963806
parameter: 963816
rule: 963707
parameter: 963814
parameter: 963742
parameter: 963748
parameter: 963758
parameter: 963838
parameter: 963848
parameter: 963846
parameter: 963836
parameter: 963776
parameter: 963786

963789
type: Parameter
constant: true
value: 10.0
name: ki_20_

963777
type: Parameter
constant: true
value: 20.0
name: epsilonc1_n3

963845
type: Parameter
constant: true
value: 0.1
name: Ja_swi

219790
type: SBMLUnitsDef
unit: 219802
name: time

219802
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

963843
type: Parameter
constant: true
value: 0.2
name: ki_swi_

963771
type: Parameter
constant: true
value: 0.05
name: kdi_b2

963781
type: Parameter
constant: true
value: 0.067
name: epsilonc1_b2

963738
type: Parameter
constant: false
value: 0.2342
name: Clb2_T

963818
type: Parameter
constant: true
value: 0.08
name: ks_spn

963828
type: Parameter
constant: true
value: 0.01
name: Ja_sbf

963756
type: Parameter
constant: true
value: 0.25
name: kd_b5_

963744
type: Parameter
constant: true
value: 2.0
name: kd_b2_

963820
type: Parameter
constant: true
value: 0.2
name: J_spn

963830
type: Parameter
constant: true
value: 75.0
name: epsilonsbf_n3

963788
type: Parameter
constant: true
value: 0.1
name: ki_20

963798
type: Parameter
constant: false
value: NaN
name: Vi_t1

963792
type: Parameter
constant: false
value: 0.9946
name: Hct1

963780
type: Parameter
constant: true
value: 1.0
name: epsilonc1_b5

963790
type: Parameter
constant: false
value: NaN
name: Vi_20

963805
type: Parameter
constant: false
value: 0.6608
name: mass

963815
type: Parameter
constant: true
value: 1.0
name: epsilonbud_b5

963749
type: Parameter
constant: false
value: NaN
name: Clb5

963757
type: Parameter
constant: false
value: NaN
name: Vd_b5

963837
type: Parameter
constant: true
value: 1.0
name: Ji_mcm

963825
type: Parameter
constant: true
value: 6.0
name: ki_sbf_

963775
type: Parameter
constant: false
value: NaN
name: Vd2_c1

963773
type: Parameter
constant: true
value: 50.0
name: kas_b5

219694
type: SBMLUnitsDef
unit: 219706
name: minute

219706
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

963795
type: Parameter
constant: true
value: 0.0
name: ki_t1

963734
type: Parameter
constant: false
value: 0.0078
name: Cln2

963822
type: Parameter
constant: true
value: 1.0
name: ka_sbf

963812
type: Parameter
constant: false
value: 0.0
name: BUD

963752
type: Parameter
constant: true
value: 0.006
name: ks_b5

963740
type: Parameter
constant: true
value: 0.002
name: ks_b2

963750
type: Parameter
constant: false
value: NaN
name: Sic1

963840
type: Parameter
constant: true
value: 1.0
name: ka_swi

963772
type: Parameter
constant: false
value: 0.0207
name: Clb5_Sic1

963782
type: Parameter
constant: false
value: 0.8332
name: Cdc20_T

219657
type: SBMLUnitsDef
unit: 219681
unit: 219669
name: nanomolar

219681
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

219669
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

963739
type: Parameter
constant: true
value: 1.0
name: Hct1_T

963737
type: Parameter
constant: true
value: 0.1
name: kd_n2

963839
type: Parameter
constant: false
value: NaN
name: Swi5

963767
type: Parameter
constant: true
value: 0.02
name: ks_c1

963755
type: Parameter
constant: true
value: 0.1
name: kd_b5

963765
type: Parameter
constant: false
value: 0.1231
name: Sic1_T

963833
type: Parameter
constant: false
value: NaN
name: Mcm1

963821
type: Parameter
constant: false
value: NaN
name: SBF

963831
type: Parameter
constant: true
value: 0.5
name: epsilonsbf_b5

963799
type: Parameter
constant: true
value: 0.05
name: Ji_t1

963806
type: Parameter
constant: true
value: 0.005776
name: mu

963816
type: Parameter
constant: false
value: 0.0
name: SPN

963814
type: Parameter
constant: true
value: 0.06
name: kd_bud

963742
type: Parameter
constant: true
value: 0.05
name: ks_b2_

963748
type: Parameter
constant: false
value: NaN
name: Clb2

963758
type: Parameter
constant: false
value: NaN
name: Bck2

963838
type: Parameter
constant: true
value: 1.0
name: Ja_mcm

963848
type: Parameter
constant: true
value: 0.08
name: kd_20

963846
type: Parameter
constant: true
value: 0.01
name: kd1_c1

963836
type: Parameter
constant: true
value: 0.15
name: ki_mcm

963776
type: Parameter
constant: true
value: 0.3
name: kd2_c1

963786
type: Parameter
constant: false
value: 0.6848
name: Cdc20

963697
type: Compartment
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0

ORG:
  orgname: University of Auckland
n:
  given: Catherine
  family: Lloyd

W3 CDTF: Fri Jun 25 13:06:06 BST 2010

963735
type: Parameter
constant: true
value: 0.0
name: ks_n2

963745
type: Parameter
constant: true
value: 0.05
name: kd_b2__

963813
type: Parameter
constant: true
value: 0.3
name: ks_bud

963763
type: Parameter
constant: true
value: 1.0
name: Dn3

963751
type: Parameter
constant: false
value: 0.0614
name: Clb5_T

963761
type: Parameter
constant: false
value: NaN
name: Cln3

963783
type: Parameter
constant: true
value: 0.005
name: ks_20

963793
type: Parameter
constant: true
value: 0.04
name: ka_t1

963808
type: Parameter
constant: true
value: 2.0
name: ks_ori

963800
type: Parameter
constant: true
value: 0.05
name: Ja_t1

963768
type: Parameter
constant: true
value: 0.1
name: ks_c1_

963844
type: Parameter
constant: true
value: 0.1
name: Ji_swi

963832
type: Parameter
constant: false
value: NaN
name: MBF

963842
type: Parameter
constant: true
value: 0.3
name: ki_swi

963770
type: Parameter
constant: true
value: 50.0
name: kas_b2

W3 CDTF: Fri Jun 25 13:06:06 BST 2010

219718
type: SBMLUnitsDef
unit: 219754
unit: 219742
unit: 219730
name: flux

219754
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

219742
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

219730
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

963827
type: Parameter
constant: true
value: 0.01
name: Ji_sbf

ORG:
  orgname: University of Auckland
n:
  given: Catherine
  family: Lloyd

963743
type: Parameter
constant: true
value: 0.01
name: kd_b2

963753
type: Parameter
constant: true
value: 0.02
name: ks_b5_

963759
type: Parameter
constant: true
value: 0.0027
name: Bck2_0

963769
type: Parameter
constant: false
value: 0.079
name: Clb2_Sic1

963849
type: Parameter
constant: true
value: 0.05
name: Jd2_c1

963787
type: Parameter
constant: true
value: 1.0
name: ka_20

219766
type: SBMLUnitsDef
unit: 219778
name: first_order_rate_constant

219778
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

963804
type: Parameter
constant: true
value: 1.0
name: epsiloni_t1_b2

963802
type: Parameter
constant: true
value: 0.5
name: epsiloni_t1_b5

963736
type: Parameter
constant: true
value: 0.05
name: ks_n2_

963746
type: Parameter
constant: false
value: NaN
name: Vd_b2

963826
type: Parameter
constant: false
value: NaN
name: Va_sbf

963834
type: Parameter
constant: true
value: 1.0
name: ka_mcm

963824
type: Parameter
constant: true
value: 0.5
name: ki_sbf

963764
type: Parameter
constant: true
value: 0.02
name: Cln3_max

963774
type: Parameter
constant: true
value: 0.05
name: kdi_b5

W3 CDTF: Fri Jun 25 13:06:06 BST 2010

963762
type: Parameter
constant: true
value: 6.0
name: Jn3

963796
type: Parameter
constant: true
value: 0.64
name: ki_t1_

963784
type: Parameter
constant: true
value: 0.06
name: ks_20_

963794
type: Parameter
constant: true
value: 2.0
name: ka_t1_

963809
type: Parameter
constant: true
value: 0.06
name: kd_ori

963819
type: Parameter
constant: true
value: 0.06
name: kd_spn

963807
type: Parameter
constant: false
value: 0.0
name: ORI

963801
type: Parameter
constant: true
value: 1.0
name: epsiloni_t1_n2

963811
type: Parameter
constant: true
value: 0.4
name: epsilonori_b2

963779
type: Parameter
constant: true
value: 2.0
name: epsilonc1_k2

W3 CDTF: Fri Jun 25 13:06:06 BST 2010

ORG:
  orgname: University of Auckland
n:
  given: Catherine
  family: Lloyd