760476
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

760946
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species: metaid_0000015
type: SpeciesReference

metaid_0000074
kinetic law: 760753
product: 760741
reactant: 760729
is version of: GO:0006468
is version of: http://identifiers.org/ec-code/2.7.1.37
fast: false
reversible: false
name: first nuclear Per phosphorylation
type: Reaction

metaid_0000009
unit: 760416
name: nanomole
type: SBMLUnitsDef

metaid_0000063
constant: true
value: 2.8249
name: Tdelay
type: Parameter

metaid_0000084
kinetic law: 760934
reactant: 760922
is version of: GO:0030163
fast: false
reversible: false
name: Per-P_cyt aspecific degradation
type: Reaction

metaid_0000053
constant: true
value: 0.38232
name: Rpdbas
type: Parameter

metaid_0000022
constant: true
value: 0.54
name: Kvc
type: Parameter

metaid_0000033
constant: true
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name: Fpd
type: Parameter

metaid_0000029
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name: Kpddeac
type: Parameter

760729
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000015
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000004
name: P2cyt
type: Species

760693
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000043
constant: true
value: 5.0
name: N
type: Parameter

761018
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000064
kinetic law: 760609
reactant: 760597
is version of: GO:0030163
fast: false
reversible: false
name: Vri specific degradation
type: Reaction

metaid_0000073
kinetic law: 760717
product: 760705
reactant: 760693
is version of: GO:0006606
fast: false
reversible: false
name: Per nuclear transport
type: Reaction

metaid_0000054
kinetic law: 760440
product: 760428
has part: GO:0006351
has part: GO:0006412
fast: false
reversible: false
name: Per production
type: Reaction

metaid_0000083
kinetic law: 760910
reactant: 760898
is version of: GO:0030163
fast: false
reversible: false
name: Per_cyt aspecific degradation
type: Reaction

760428
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000021
constant: true
value: 0.1
name: Kppd
type: Parameter

760777
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000016
is: O18660
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000003
name: VRI
type: Species

metaid_0000072
kinetic law: 760681
product: 760669
reactant: 760657
is version of: GO:0006468
is version of: http://identifiers.org/ec-code/2.7.1.37
fast: false
reversible: false
name: second cytoplasmic Per phosphorylation
type: Reaction

metaid_0000065
constant: true
value: 1.6992
name: Vpcyt
type: Parameter

760501
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000010
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000003
name: P0nuc
type: Species

metaid_0000051
constant: true
value: 0.19116
name: Rvbas
type: Parameter

metaid_0000020
constant: true
value: 0.24
name: Kpp
type: Parameter

metaid_0000086
kinetic law: 760982
reactant: 760970
is version of: GO:0030163
fast: false
reversible: false
name: Per_nuc aspecific degradation
type: Reaction

760825
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000027
constant: true
value: 0.2124
name: Kvdeac
type: Parameter

metaid_0000031
constant: true
value: 1.062
name: Fv
type: Parameter

metaid_0000017
constant: false
initial amount: NaN
in compartment: metaid_0000003
name: CLK
initial concentration: 0.001
has part: P07663
type: Species
has part: O61735
has only substance units: false
boundary condition: false

metaid_0000007
constant: false
value: NaN
name: ACpdp
type: Parameter

metaid_0000071
kinetic law: 760645
product: 760633
reactant: 760621
is version of: GO:0006468
is version of: http://identifiers.org/ec-code/2.7.1.37
fast: false
reversible: false
name: first cytoplasmic Per phosphorylation
type: Reaction

metaid_0000066
constant: true
value: 0.25
name: Kpcyt
type: Parameter

metaid_0000039
constant: true
value: 2.8249
name: Tvriop
type: Parameter

metaid_0000085
kinetic law: 760958
reactant: 760946
is version of: GO:0030163
fast: false
reversible: false
name: Per-PP_cyt aspecific degradation
type: Reaction

760633
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000052
constant: true
value: 0.001062
name: Rcbas
type: Parameter

760765
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000028
constant: true
value: 0.2124
name: Kpdeac
type: Parameter

metaid_0000046
constant: true
value: 10.62
name: Vper
type: Parameter

metaid_0000059
constant: true
value: 0.7434
name: vdvri
type: Parameter

metaid_0000032
constant: true
value: 1.062
name: Fp
type: Parameter

760970
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

760416
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

760898
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000079
kinetic law: 760837
reactant: 760825
is version of: GO:0030163
fast: false
reversible: false
name: Clk aspecific degradation
type: Reaction

metaid_0000018
is: Q9TVS7
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000003
name: PDP
type: Species

metaid_0000008
unit: 760404
name: hour
type: SBMLUnitsDef

760573
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

760549
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000067
constant: true
value: 0.3186
name: Vpnuc
type: Parameter

metaid_0000005
constant: false
value: NaN
name: ACvri
type: Parameter

760705
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000019
constant: true
value: 0.2
name: Kpv
type: Parameter

metaid_0000038
constant: false
value: NaN
name: OPpdp
type: Parameter

metaid_0000048
constant: true
value: 344.09
name: Vpdp
type: Parameter

760922
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000070
constant: true
value: 0.25
name: Ktrans
type: Parameter

metaid_0000057
name: Clk production
kinetic law: 760537
modifier: 760525
has part: GO:0006351
has part: GO:0006412
fast: false
product: 760501
reversible: false
type: Reaction
modifier: 760513

760669
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000078
kinetic law: 760813
reactant: 760801
is version of: GO:0030163
fast: false
reversible: false
name: Per specific degradation
type: Reaction

metaid_0000088
kinetic law: 761030
reactant: 761018
is version of: GO:0030163
fast: false
reversible: false
name: Per-PP_nuc aspecific degradation
type: Reaction

760850
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

metaid_0000025
constant: true
value: 0.134
name: Kcp
type: Parameter

metaid_0000011
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000003
name: P1nuc
type: Species

BIOMD0000000034
parameter: metaid_0000047
reaction: metaid_0000072
reaction: metaid_0000078
volume units: metaid_0000323
name: Smolen2004_CircClock
parameter: metaid_0000066
notes: No inititial conditions are specified in the paper. Because there is a basal rate of transcription for each gene, it doesn't matter much. With the agreement of Paul Smolen, I put all the initial concentration at 0.001 nanomoles. N Le Novère. 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.
occurs in: http://identifiers.org/taxonomy/7227
reaction: metaid_0000071
reaction: metaid_0000054
species: metaid_0000013
parameter: metaid_0000050
parameter: metaid_0000005
type: SBMLModel
parameter: metaid_0000053
parameter: metaid_0000039
reaction: metaid_0000082
parameter: metaid_0000041
parameter: metaid_0000080
parameter: metaid_0000067
parameter: metaid_0000040
parameter: metaid_0000046
area units: area
species: metaid_0000017
parameter: metaid_0000023
is: MODEL6619579403
parameter: metaid_0000038
parameter: metaid_0000029
parameter: metaid_0000033
reaction: metaid_0000083
parameter: metaid_0000037
parameter: metaid_0000028
is described by: http://identifiers.org/pubmed/15111397
parameter: metaid_0000077
species: metaid_0000014
reaction: metaid_0000088
is version of: GO:0007623
compartment: metaid_0000004
parameter: metaid_0000065
reaction: metaid_0000064
rule: metaid_0000044
parameter: metaid_0000060
parameter: metaid_0000019
curated: true
reaction: metaid_0000075
parameter: metaid_0000052
parameter: metaid_0000007
parameter: metaid_0000058
reaction: metaid_0000057
reaction: metaid_0000081
parameter: metaid_0000022
parameter: metaid_0000051
rule: metaid_0000045
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reaction: metaid_0000086
species: metaid_0000018
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reaction: metaid_0000062
reaction: metaid_0000074
parameter: metaid_0000048
reaction: metaid_0000073
species: metaid_0000015
time units: metaid_0000008
parameter: metaid_0000032
parameter: metaid_0000036
parameter: metaid_0000027
species: metaid_0000011
parameter: metaid_0000076
parameter: metaid_0000031
parameter: metaid_0000006
reaction: metaid_0000087
compartment: metaid_0000003
species: metaid_0000012
is: dme04710
units def: metaid_0000008
rule: metaid_0000035
species: metaid_0000010
parameter: metaid_0000063
length unit: length
parameter: metaid_0000069

metaid_0000006
constant: false
value: NaN
name: ACper
type: Parameter

760404
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

metaid_0000068
constant: true
value: 0.001
name: Kpnuc
type: Parameter

metaid_0000037
constant: false
value: NaN
name: OPper
type: Parameter

metaid_0000058
constant: true
value: 0.2124
name: Vdclk
type: Parameter

metaid_0000047
constant: true
value: 76.464
name: Vvri
type: Parameter

metaid_0000012
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000003
name: P2nuc
type: Species

metaid_0000040
constant: true
value: 2.8249
name: Tperop
type: Parameter

metaid_0000087
kinetic law: 761006
reactant: 760994
is version of: GO:0030163
fast: false
reversible: false
name: Per-P_nuc aspecific degradation
type: Reaction

metaid_0000050
constant: true
value: 0.02124
name: Rpbas
type: Parameter

760621
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000077
constant: true
value: 0.01
name: Kdegp
type: Parameter

metaid_0000060
constant: true
value: 0.6903
name: vdpdp
type: Parameter

760452
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000026
constant: true
value: 0.248
name: Kcpd
type: Parameter

metaid_0000003
is: GO:0005634
constant: true
size: 1.0
spatial dimensions: 3.0
name: nucleus
type: Compartment

metaid_0000069
constant: true
value: 1.6992
name: Vtrans
type: Parameter

metaid_0000055
kinetic law: 760464
product: 760452
has part: GO:0006351
has part: GO:0006412
fast: false
reversible: false
name: Vri production
type: Reaction

metaid_0000036
constant: false
value: NaN
name: OPvri
type: Parameter

metaid_0000082
kinetic law: 760886
reactant: 760874
is version of: GO:0030163
fast: false
reversible: false
name: Vri aspecific degradation
type: Reaction

metaid_0000041
constant: true
value: 2.8249
name: Tpdpop
type: Parameter

metaid_0000013
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000004
name: P0cyt
type: Species

760657
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000023
constant: true
value: 0.54
name: Kpdc
type: Parameter

760801
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000061
kinetic law: 760561
reactant: 760549
is version of: GO:0030163
fast: false
reversible: false
name: Clk specific degradation
type: Reaction

metaid_0000076
constant: true
value: 5.31
name: Vdegp
type: Parameter

760597
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000004
is: GO:0005737
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

metaid_0000081
kinetic law: 760862
reactant: 760850
is version of: GO:0030163
fast: false
reversible: false
name: Pdp aspecific degradation
type: Reaction

760741
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000056
kinetic law: 760489
product: 760476
has part: GO:0006351
has part: GO:0006412
fast: false
reversible: false
name: Pdp production
type: Reaction

760994
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000049
constant: true
value: 1.062
name: Vclk
type: Parameter

760874
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000014
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.001
initial amount: NaN
in compartment: metaid_0000004
name: P1cyt
type: Species

metaid_0000024
constant: true
value: 0.083
name: Kcv
type: Parameter

metaid_0000080
constant: true
value: 0.00531
name: kd
type: Parameter

metaid_0000062
kinetic law: 760585
reactant: 760573
is version of: GO:0030163
fast: false
reversible: false
name: Pdp specific degradation
type: Reaction

metaid_0000075
kinetic law: 760789
product: 760777
reactant: 760765
is version of: GO:0006468
is version of: http://identifiers.org/ec-code/2.7.1.37
fast: false
reversible: false
name: second nuclear Rer phosphorylation
type: Reaction

W3 CDTF: Fri Jun 24 13:05:27 BST 2005

given: Nicolas
family: Le Novère

ORG:
  orgname: EMBL-EBI

W3 CDTF: Thu Jul 05 15:42:52 BST 2012