BIOMD0000000111
type: SBMLModel
reaction: metaid_0000090
parameter: metaid_0000035
parameter: metaid_0000036
parameter: metaid_0000008
reaction: metaid_0000084
reaction: metaid_0000075
reaction: metaid_0000076
species: metaid_0000065
reaction: metaid_0000079
length unit: length
species: metaid_0000094
volume units: metaid_0000084
species: metaid_0000059
area units: metaid_0000005
event: metaid_0000098
species: metaid_0000062
parameter: metaid_0000042
notes: The model reproduces the time evolution of several species as depicted in Fig 4 of the paper. Events have been used to reset cell mass when the value of M-phase promoting factor (MPF) decreases through 0.1. The model was successfully tested on Cell Designer. 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.
parameter: metaid_0000033
parameter: metaid_0000034
parameter: metaid_0000025
reaction: metaid_0000074
reaction: metaid_0000073
parameter: metaid_0000027
units def: metaid_0020097
units def: metaid_0000097
rule: metaid_0000069
parameter: metaid_0000051
parameter: metaid_0000013
parameter: metaid_0000052
parameter: metaid_0000014
parameter: metaid_0000093
parameter: metaid_0000043
parameter: metaid_0000015
parameter: metaid_0000049
parameter: metaid_0000016
parameter: metaid_0000024
parameter: metaid_0000007
name: Novak2001_FissionYeast_CellCycle
reaction: metaid_0000083
reaction: metaid_0000089
species: metaid_0000066
parameter: metaid_0000048
is version of: spo04111
reaction: metaid_0000088
species: metaid_0000063
is: MODEL6488296959
parameter: metaid_0000050
parameter: metaid_0000041
parameter: metaid_0000022
parameter: metaid_0000005
rule: metaid_0000067
event: metaid_0000096
species: metaid_0000060
rule: metaid_0000071
parameter: metaid_0000040
substance units: metaid_0020097
reaction: metaid_0000082
parameter: metaid_0000031
parameter: metaid_0000046
parameter: metaid_0000032
parameter: metaid_0000004
parameter: metaid_0000037
parameter: metaid_0000023
parameter: metaid_0000038
reaction: metaid_0000086
parameter: metaid_0000039
reaction: metaid_0000077
reaction: metaid_0000078
compartment: metaid_0000056
parameter: metaid_0000011
parameter: metaid_0000012
parameter: metaid_0000055
reaction: metaid_0000091
parameter: metaid_0000047
parameter: metaid_0000019
occurs in: http://identifiers.org/taxonomy/4894
reaction: metaid_0000087
time units: metaid_0000095

metaid_0000090
type: Reaction
kinetic law: 265317
reactant: 265305
is: GO:0044257
fast: false
reversible: false
name: SK degradation

265305
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000065

metaid_0000065
type: Species
is version of: P24865
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000056
name: SK

metaid_0000056
type: Compartment
is: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

metaid_0000035
type: Parameter
constant: true
units: metaid_0000097
value: 35.0

metaid_0000097
type: SBMLUnitsDef
unit: 264691
name: min_inv

264691
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000036
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000008
type: Parameter
constant: true
units: metaid_0000097
value: 1.5

metaid_0000084
type: Reaction
kinetic law: 265137
reactant: 265125
is: GO:0044257
fast: false
reversible: false
name: slp1 inactivation

265125
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000062
type: Species
is: P78972
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 2.2
in compartment: metaid_0000056
name: slp1

metaid_0000075
type: Reaction
is: GO:0018108
reversible: false
modifier: 264812
kinetic law: 264824
is version of: REACT 6178
name: wee1 dependent MPF inactivation
is: GO:0045736
fast: false
product: 264800
is: http://identifiers.org/ec-code/2.7.10.2

metaid_0000058
type: Species
is version of: IPR015454
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.2
in compartment: metaid_0000056
name: Total cdc13

264800
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000059
type: Species
in compartment: metaid_0000056
boundary condition: false
has part: IPR015454
initial concentration: NaN
constant: false
has only substance units: true
initial amount: 0.0
name: preMPF
has part: P04551

metaid_0000076
type: Reaction
kinetic law: 264848
is: GO:0004725
is version of: REACT 6257.1
reversible: false
fast: false
is: GO:0010389
name: cdc25 dependent preMPF phosphorylation
reactant: 264837
is: http://identifiers.org/ec-code/3.1.3.48

264837
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000079
type: Reaction
kinetic law: 264981
modifier: 264968
modifier: 264957
reactant: 264945
is: GO:0006468
fast: false
reversible: false
name: ste9 phosphorylation (inactivation) by starter kinase

metaid_0000094
type: Species
constant: false
name: M-phase promoting factor
in compartment: metaid_0000056
boundary condition: false
has part: IPR015454
initial amount: 0.0
has part: P04551
initial concentration: NaN
has only substance units: true

264945
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000060

metaid_0000060
type: Species
is: O13286
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 1.0
in compartment: metaid_0000056
name: ste9

metaid_0000098
type: Event
event assignment: 265402
trigger: 265390
use values from trigger time: true

metaid_0000093
type: Parameter
constant: false
units: dimensionless
value: 0.0

265390
type: Trigger
persistant: true
initial value: true

metaid_0000042
type: Parameter
constant: true
units: dimensionless
value: 0.001

metaid_0000033
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000034
type: Parameter
constant: true
units: metaid_0000097
value: 2.0

metaid_0000025
type: Parameter
constant: true
units: metaid_0000097
value: 0.25

metaid_0000074
type: Reaction
reactant: 264751
modifier: 264764
name: Targeting cdc13T to APC core
is: GO:0007092
fast: false
reversible: false
modifier: 264776
is: GO:0008054
kinetic law: 264788

264751
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000058

metaid_0000073
type: Reaction
kinetic law: 264739
modifier: 264727
product: 264715
is: GO:0006412
is: GO:0007346
fast: false
reversible: false
name: cdc13T synthesis

metaid_0000066
type: Species
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 1.0
in compartment: metaid_0000056
name: Cell Mass

264715
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000058

metaid_0000027
type: Parameter
constant: true
units: metaid_0000097
value: 0.03

metaid_0020097
type: SBMLUnitsDef
unit: 264703
name: norm. substance

264703
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS

metaid_0000051
type: Parameter
constant: true
units: metaid_0000097
value: 1.0

metaid_0000013
type: Parameter
constant: false
units: metaid_0000097
value: 0.0

metaid_0000052
type: Parameter
constant: true
units: metaid_0000097
value: 3.0

metaid_0000014
type: Parameter
constant: true
units: metaid_0000097
value: 0.15

metaid_0000043
type: Parameter
constant: true
units: metaid_0000097
value: 0.25

metaid_0000015
type: Parameter
constant: true
units: metaid_0000097
value: 1.3

metaid_0000049
type: Parameter
constant: true
units: metaid_0000097
value: 0.1

metaid_0000016
type: Parameter
constant: true
units: metaid_0000097
value: 0.25

metaid_0000024
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000007
type: Parameter
constant: false
units: dimensionless
value: 0.0

metaid_0000083
type: Reaction
kinetic law: 265113
reactant: 265101
is: GO:0044257
fast: false
reversible: false
name: slp1 inactivation

265101
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000089
type: Reaction
kinetic law: 265293
product: 265281
is: GO:0006412
fast: false
reversible: false
name: SK synthesis

265281
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000065

metaid_0000048
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000088
type: Reaction
kinetic law: 265269
modifier: 265257
modifier: 265245
reactant: 265233
is: GO:0031657
fast: false
reversible: false
name: SK dependent rum1T inactivation

265233
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000064

metaid_0000064
type: Species
is: P40380
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000056
name: rum1T

metaid_0000063
type: Species
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000056
name: IEP

metaid_0000050
type: Parameter
constant: true
units: metaid_0000097
value: 0.01

metaid_0000041
type: Parameter
constant: true
units: metaid_0000097
value: 1.0

metaid_0000022
type: Parameter
constant: true
units: metaid_0000097
value: 5.0

metaid_0000005
type: Parameter
constant: false
units: dimensionless
value: 0.0

metaid_0000096
type: Event
event assignment: 265378
event assignment: 265366
trigger: 265353
notes: The two events are used to reset the cell mass (divide by two) when MPF decreases through 0.1
use values from trigger time: true

265353
type: Trigger
persistant: true
initial value: true

metaid_0000040
type: Parameter
constant: true
units: metaid_0000097
value: 0.1

metaid_0000082
type: Reaction
kinetic law: 265089
modifier: 265077
modifier: 265065
product: 265053
is: GO:0051443
fast: false
reversible: false
name: slp1 activation by intermediary enzyme

metaid_0000061
type: Species
is: P78972
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000056
name: slp1T

265053
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000031
type: Parameter
constant: true
units: metaid_0000097
value: 1.0

metaid_0000046
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000032
type: Parameter
constant: true
units: metaid_0000097
value: 10.0

metaid_0000004
type: Parameter
constant: true
units: dimensionless
value: 0.001

metaid_0000037
type: Parameter
constant: true
units: metaid_0000097
value: 0.005

metaid_0000023
type: Parameter
constant: true
units: metaid_0000097
value: 1.0

metaid_0000038
type: Parameter
constant: true
units: metaid_0000097
value: 0.3

metaid_0000086
type: Reaction
kinetic law: 265197
reactant: 265185
is: GO:0006470
fast: false
reversible: false
name: IEP inactivation

265185
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000063

metaid_0000039
type: Parameter
constant: true
units: dimensionless
value: 0.3

metaid_0000077
type: Reaction
is: GO:0007092
is: GO:0008054
name: preMPF inactivation
is: GO:0000216
reversible: false
fast: false
modifier: 264872
reactant: 264860
modifier: 264885
kinetic law: 264897

264860
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000078
type: Reaction
kinetic law: 264933
modifier: 264921
product: 264909
is: GO:0035307
fast: false
reversible: false
name: slp1 dependent ste9 activation

264909
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000060

metaid_0000011
type: Parameter
constant: true
units: metaid_0000097
value: 2.0

metaid_0000012
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000055
type: Parameter
constant: true
units: metaid_0000097
value: 0.005

metaid_0000091
type: Reaction
kinetic law: 265341
product: 265329
is: GO:0016049
fast: false
reversible: false
name: Cell growth

265329
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

metaid_0000047
type: Parameter
constant: true
units: metaid_0000097
value: 0.04

metaid_0000019
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000087
type: Reaction
kinetic law: 265221
product: 265209
is: GO:0031657
fast: false
reversible: false
name: rum1T activation

265209
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000064

metaid_0000095
type: SBMLUnitsDef
unit: 264677
name: minutes

264677
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000030
type: Parameter
constant: true
units: metaid_0000097
value: 0.1

metaid_0000021
type: Parameter
constant: true
units: metaid_0000097
value: 0.05

metaid_0000029
type: Parameter
constant: true
units: metaid_0000097
value: 1.0

metaid_0000010
type: Parameter
constant: true
units: metaid_0000097
value: 1.0

W3 CDTF: Fri Apr 13 06:35:42 BST 2007

metaid_0000053
type: Parameter
constant: true
units: metaid_0000097
value: 0.1

metaid_0000081
type: Reaction
kinetic law: 265041
reactant: 265029
is: GO:0044257
fast: false
reversible: false
name: slp1T inactivation

265029
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000061

metaid_0000054
type: Parameter
constant: true
units: metaid_0000097
value: 0.1

metaid_0000080
type: Reaction
kinetic law: 265017
modifier: 265005
product: 264993
is: GO:0006468
fast: false
reversible: false
name: slp1T activation by MPF

264993
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000061

metaid_0000045
type: Parameter
constant: true
units: metaid_0000097
value: 0.1

metaid_0000020
type: Parameter
constant: false
units: metaid_0000097
value: 0.0

metaid_0000017
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000003
type: Parameter
constant: false
units: dimensionless
value: 0.0

metaid_0000018
type: Parameter
constant: true
units: metaid_0000097
value: 1.0

metaid_0000026
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000009
type: Parameter
constant: true
units: dimensionless
value: 0.01

metaid_0000085
type: Reaction
kinetic law: 265173
modifier: 265161
product: 265149
is: GO:0006468
fast: false
reversible: false
name: Intermediary enzyme activation

265149
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000063

metaid_0000028
type: Parameter
constant: true
units: metaid_0000097
value: 0.03

metaid_0000044
type: Parameter
constant: true
units: dimensionless
value: 0.001

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri

W3 CDTF: Thu Jul 05 17:47:55 BST 2012