536707
value: 0.3
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type: LocalParameter

536716
value: 0.2
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type: LocalParameter

536726
value: 2.0
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is version of: GO:0044257
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type: Reaction

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value: 4.4
name: vdrc
type: LocalParameter

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stoichiometry: 1.0
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metaid_0000043
is version of: GO:0006468
fast: false
reversible: false
name: PCc phospholation
type: Reaction

536706
value: 3.0
name: vdbn
type: LocalParameter

536717
value: 0.1
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type: LocalParameter

536727
value: 0.6
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type: LocalParameter

metaid_0000084
is version of: GO:0008233
fast: false
reversible: false
name: Rn specific degradation
type: Reaction

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stoichiometry: 1.0
species: metaid_0000020
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536649
value: 3.2
name: ksc
type: LocalParameter

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metaid_0000056
is version of: GO:0044257
fast: false
reversible: false
name: Pc nonspecific degradation
type: Reaction

metaid_0000017
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boundary condition: false
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name: Mp
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is version of: CHEBI:33699
encodes: O15534
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constant: false
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536737
value: 0.3
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stoichiometry: 1.0
species: metaid_0000027
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metaid_0000042
is version of: GO:0043623
fast: false
reversible: true
name: Cc and Pc produce PCc
type: Reaction

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reaction: metaid_0000036
reaction: metaid_0000061
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reaction: metaid_0000039
rule: metaid_0000090
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notes: This is model is according to the paper Toward a detailed computational model for the mammalian circadian clock In this model interlocked negative and positive regulation of Per,Cry,Bmal,REV-ERBalpha genes are all involved.The model is actually robust so the initial conditions are unimportant.We gave every entity zero as initial value,and start the graph at time=132h. The simulation results in figure 8B can be reproduced by roadRunner online and Copasi. We use a ceiling function to simulate the day-light cycle. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use . 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.
area units: metaid_0000005
reaction: metaid_0000043
reaction: metaid_0000065
reaction: metaid_0000062
reaction: metaid_0000055
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reaction: metaid_0000077
units def: metaid_0000008
reaction: metaid_0000069
reaction: metaid_0000063
name: Leloup2003_CircClock_LD_REV-ERBalpha
is described by: http://identifiers.org/pubmed/12775757
species: metaid_0000021
reaction: metaid_0000075
reaction: metaid_0000037
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name: ceiling
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reaction: metaid_0000068
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reaction: metaid_0000082
name: Activation of gene
function def: metaid_0000005
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reaction: metaid_0000044
reaction: metaid_0000045
occurs in: http://identifiers.org/taxonomy/40674
type: SBMLModel
curated: true
species: metaid_0000018
time units: metaid_0000007
is: MODEL4710748444
length unit: length
reaction: metaid_0000064
parameter: metaid_0000088
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parameter: metaid_0000089
is version of: GO:0007623
reaction: metaid_0000030
name: mRNA translated into protein
reaction: metaid_0000040
name: Michaelis-Menten (irreversible)
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reaction: metaid_0000038
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stoichiometry: 1.0
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536714
value: 0.4
name: V4b
type: LocalParameter

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536709
value: 1.6
name: vdin
type: LocalParameter

metaid_0000083
is version of: GO:0044257
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name: Rc nonspecific degradation
type: Reaction

536728
value: 0.02
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stoichiometry: 1.0
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metaid_0000055
is version of: GO:0008233
fast: false
reversible: false
name: Mp specific degradation
type: Reaction

metaid_0000045
is version of: GO:0000060
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name: PCc transfered into nuclear
type: Reaction

metaid_0000014
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value: 0.1
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536708
value: 0.02
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536729
value: 1.6
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type: LocalParameter

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metaid_0000054
is version of: GO:0008233
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has only substance units: false

metaid_0000044
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536735
value: 0.4
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type: LocalParameter

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type: Species

536722
value: 0.02
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type: LocalParameter

metaid_0000067
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reversible: false
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type: Reaction

536712
value: 0.2
name: V2b
type: LocalParameter

536662
value: 1.006
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type: LocalParameter

536677
value: 0.6
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type: LocalParameter

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stoichiometry: 1.0
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metaid_0000047
is version of: GO:0044257
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type: Reaction

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536678
value: 2.4
name: V3pc
type: LocalParameter

536721
value: 0.1
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type: LocalParameter

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stoichiometry: 1.0
species: metaid_0000013
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metaid_0000088
constant: false
value: NaN
name: LD
type: Parameter

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536723
value: 0.2
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type: LocalParameter

metaid_0000027
has version: Q6EEZ7
constant: false
boundary condition: false
has only substance units: false
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initial amount: NaN
in compartment: metaid_0000009
name: Rc
type: Species

metaid_0000066
is version of: GO:0008233
fast: false
reversible: false
name: Bnp specific degradation
type: Reaction

536713
value: 0.1
name: Kdp
type: LocalParameter

536663
value: 0.8
name: k3
type: LocalParameter

536676
value: 2.0
type: LocalParameter

metaid_0000046
is version of: GO:0044257
fast: false
reversible: false
name: PCnp nonspecific degradation
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name: Rn
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536724
value: 0.1
name: Kdp
type: LocalParameter

metaid_0000079
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fast: false
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name: Mr specific degradation
type: Reaction

metaid_0000059
is version of: GO:0044257
fast: false
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name: Ccp nonspecific degradation
type: Reaction

metaid_0000087
notes: when LD=0, it is night,when LD=1,it is day
is version of: GO:0007623

536660
value: 0.3
name: Kd
type: LocalParameter

metaid_0000049
is part of: GO:0045893
fast: false
reversible: false
name: Mc synthesis
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536638
value: 1.0
name: Kib
type: LocalParameter

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exponent: 1.0
scale: 0
multipler: 3600.0
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type: SBMLUnit

metaid_0000038
is version of: GO:0045893
fast: false
reversible: false
name: Mp synthesis
type: Reaction

metaid_0000069
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metaid_0000018
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type: Species
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536738
value: 0.02
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type: LocalParameter

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536725
value: 1.6
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type: LocalParameter

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is version of: GO:0044257
fast: false
reversible: false
name: Mr nonspecific degradation
type: Reaction

536651
value: 0.02
name: kdmc
type: LocalParameter

536688
value: 0.3
name: Kmp
type: LocalParameter

metaid_0000058
is version of: GO:0044257
fast: false
reversible: false
name: Pcp nonspecific degradation
type: Reaction

metaid_0000029
is version of: GO:0045892
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reversible: false
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type: Reaction

metaid_0000048
is version of: GO:0044257
fast: false
reversible: false
name: Bnp nonspecific degradation
type: Reaction

536661
value: 9.6
name: V1p
type: LocalParameter

536711
value: 0.02
name: kdn
type: LocalParameter

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stoichiometry: 1.0
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metaid_0000039
is version of: GO:0006412
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reversible: false
name: Mp translated into protein
type: Reaction

metaid_0000068
is version of: GO:0008233
fast: false
reversible: false
name: In specific degradation
type: Reaction

536637
value: 1.8
name: vsb
type: LocalParameter

metaid_0000019
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name: Pcp
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has version: O15534
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has only substance units: false

536710
value: 0.3
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type: LocalParameter

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stoichiometry: 1.0
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536679
value: 1.006
name: Kp
type: LocalParameter

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536689
value: 0.02
name: kdn
type: LocalParameter

metaid_0000009
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell
type: Compartment

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536691
value: 0.02
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type: LocalParameter

metaid_0000022
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species: metaid_0000027
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536730
value: 0.4
name: Kmr
type: LocalParameter

536720
value: 0.2
name: V4pc
type: LocalParameter

536693
value: 0.02
name: kdn
type: LocalParameter

536667
value: 1.4
name: vdpcc
type: LocalParameter

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stoichiometry: 1.0
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metaid_0000036
is version of: GO:0006468
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reversible: false
name: Cc phosphorylation
type: Reaction

536666
value: 1.006
name: Kp
type: LocalParameter

536673
value: 0.02
name: kdn
type: LocalParameter

536740
value: 0.8
name: vdrn
type: LocalParameter

metaid_0000062
is version of: GO:0008233
fast: false
reversible: false
name: PCnp specific degradation
type: Reaction

536647
value: 0.8
name: k5
type: LocalParameter

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536687
value: 2.2
name: vmp
type: LocalParameter

metaid_0000076
is version of: GO:0006470
fast: false
reversible: false
name: PCcp dephospholation
type: Reaction

536652
value: 1.2
name: V1c
type: LocalParameter

metaid_0000023
has version: O00327
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name: Bnp
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536692
value: 0.02
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536668
value: 0.3
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type: LocalParameter

metaid_0000063
is version of: GO:0044257
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metaid_0000037
is version of: GO:0008233
fast: false
reversible: false
name: Ccp specific degradation
type: Reaction

536648
value: 0.4
name: k6
type: LocalParameter

536686
value: 0.4
name: Kmc
type: LocalParameter

metaid_0000077
is part of: GO:0045893
fast: false
reversible: false
name: Mr synthesized
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536653
value: 1.006
name: Kp
type: LocalParameter

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metaid_0000024
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has part: Q16526
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constant: false
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has only substance units: false
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has part: Q8IV71
has part: O15534

metaid_0000034
is version of: GO:0006412
fast: false
reversible: false
name: Mc translated into protein
type: Reaction

536644
value: 1.4
name: V1b
type: LocalParameter

536695
value: 0.02
name: kdn
type: LocalParameter

536701
value: 0.3
name: Kd
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_52d64825_cc2e_4c1c_be85_abbef2054893
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

536675
value: 2.2
name: vsc
type: LocalParameter

metaid_0000064
is version of: GO:0008233
fast: false
reversible: false
name: Bcp specific degradation
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#_8d3193ea_f457_4de8_9c80_de4eda4df2c6
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

536664
value: 0.4
name: k4
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#b58c6a1d_ddff_4103_b3f1_73e985b1876c
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

metaid_0000074
is version of: GO:0006470
fast: false
reversible: false
name: PCnp dephospholation
type: Reaction

536654
value: 1.4
name: vdcc
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_5fcaad3d_c946_4c63_ae7d_547eb698847d
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000083#_90880970_16eb_4748_98ee_8a3824b1c23b
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000083#_7c3d5ccd_a933_49a9_891f_7392c59395fe
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

536685
value: 2.0
name: vmc
type: LocalParameter

536733
value: 0.8
name: k9
type: LocalParameter

536731
value: 1.7
name: ksr
type: LocalParameter

536656
value: 2.0
type: LocalParameter

metaid_0000035
is version of: GO:0044257
fast: false
reversible: false
name: Mc nonspecific degradation
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#_64c1eaf9_693e_454a_9d3b_1b69e76d120b
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000083#d40d62cd_da5d_453d_97c2_dc3114528386
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

536674
value: 0.02
name: kdn
type: LocalParameter

metaid_0000065
is version of: GO:0006468
fast: false
reversible: false
name: Bn phospholation
type: Reaction

536646
value: 1.006
name: Kp
type: LocalParameter

536700
value: 3.0
name: vdbc
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_15a1fbf1_1f70_4050_934c_ed00c7971e87
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000083#d711defc_f523_44a6_bf21_87508b734207
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

536665
value: 2.4
name: V1pc
type: LocalParameter

metaid_0000025
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000009
name: In
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000083#_61702592_4322_4d8f_a4d2_eda4466042be
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000075
is version of: GO:0044257
fast: false
reversible: false
name: PCn nonspecific degradation
type: Reaction

536655
value: 0.3
name: Kd
type: LocalParameter

536684
value: 0.4
name: Kmb
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#e626c01a_937b_4f09_ba17_98cba36123f8
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

metaid_0000032
is version of: GO:0006468
fast: false
reversible: false
name: Bc phosphorylation
type: Reaction

536697
value: 1.4
name: vdpcn
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_8463b04b_910f_40af_bf1d_a89fb47abacb
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

536657
value: 0.6
name: Kap
type: LocalParameter

W3 CDTF: Thu Oct 19 11:21:38 BST 2006

metaid_0000052
is version of: GO:0043623
fast: false
reversible: true
name: Per_Cry and Clock_Bmal form inactive complex
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#_129cd959_8e12_4921_86d3_e84e4b000b7d
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

536683
value: 1.3
name: vmb
type: LocalParameter

metaid_0000072
is part of: GO:0006470
fast: false
reversible: false
name: Ccp dephospholation
type: Reaction

metaid_0000081
is version of: GO:0000060
fast: false
reversible: true
name: Rc transfered into nuclear
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#f9c08808_034c_4ebe_9aac_b8542c3e191f
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000012
has version: O00327
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000009
name: Bcp
type: Species

536703
value: 1.4
name: V3b
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_097702de_22dc_47c2_a692_f745fddd6ec4
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

536643
value: 0.02
name: kdmb
type: LocalParameter

536696
value: 0.02
name: kdn
type: LocalParameter

metaid_0000033
is version of: GO:0000060
fast: false
reversible: true
name: Bc transfered from cytosolic to nuclear
type: Reaction

536658
value: 1.2
name: ksp
type: LocalParameter

metaid_0000053
is version of: GO:0008233
fast: false
reversible: false
name: Mb specific degradation
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#_07deaf3d_431c_4bb9_8bd4_a2e4addcad61
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

536682
value: 0.2
name: k8
type: LocalParameter

metaid_0000073
is version of: GO:0006470
fast: false
reversible: false
name: Pcp dephospholation
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#_91ece79f_75a3_40ca_afe7_8ab3ed3e24a5
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

metaid_0000090
notes: when LD=0 (night), vsp =2.4; when LD=1(day),vsp =3.

http://identifiers.org/biomodels.db/BIOMD0000000083#_2ac8588a_183f_496f_94f9_f42d5d862ca4
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000083#_2a154a76_e13b_45c8_95b2_a8575717f018
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000080
is version of: GO:0006412
fast: false
reversible: false
name: Mr translated into protein
type: Reaction

536743
value: 0.02
name: kdn
type: LocalParameter

metaid_0000013
has version: O00327
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000009
name: Bn
type: Species

536669
value: 0.8
name: k1
type: LocalParameter

536699
value: 0.02
name: kdn
type: LocalParameter

536640
value: 2.0
name: m
type: LocalParameter

metaid_0000030
is version of: GO:0006412
fast: false
reversible: false
name: Mb translated into protein
type: Reaction

metaid_0000040
is version of: GO:0008233
fast: false
reversible: false
name: Pcp specific degradation
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#_13a060e0_1349_46d6_a60b_1ac5435b0fd4
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

metaid_0000050
is version of: GO:0006468
fast: false
reversible: false
name: PCn phospholation
type: Reaction

metaid_0000020
initial amount: NaN
type: Species
initial concentration: 0.0
has part: Q16526
constant: false
has part: Q8IV71
in compartment: metaid_0000009
boundary condition: false
name: PCc
has only substance units: false
has part: P56645
has part: O15534

536659
value: 3.4
name: vdpc
type: LocalParameter

metaid_0000060
is version of: GO:0044257
fast: false
reversible: false
name: PCcp nonspecific degradation
type: Reaction

536681
value: 1.0
name: k7
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_2334119d_3999_4fd8_993d_b0d280b7ac20
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000010
encodes: O00327
initial concentration: 0.0
has only substance units: false
is version of: CHEBI:33699
name: Mb
boundary condition: false
initial amount: NaN
in compartment: metaid_0000009
constant: false
type: Species

536718
value: 0.6
name: V2p
type: LocalParameter

536742
value: 0.3
name: Kd
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_753ee7a1_753d_4da1_b68d_3c02bbaa1dcc
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000070
is version of: GO:0006470
fast: false
reversible: false
name: Bcp dephospholation
type: Reaction

536705
value: 1.006
name: Kp
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_8e22f9f1_9d72_4e42_876e_ee588a271922
stoichiometry: 1.0
species: metaid_0000026
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000083#b864c3fd_7b8b_44e1_b3fc_48a8563dad55
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

536671
value: 0.02
name: kdn
type: LocalParameter

536698
value: 0.3
name: Kd
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#_38d003ff_ca04_46f1_999e_43749e02a903
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

536641
value: 0.32
name: ksb
type: LocalParameter

metaid_0000031
is version of: GO:0044257
fast: false
reversible: false
name: Mb nonspecific degradation
type: Reaction

metaid_0000041
is version of: GO:0006468
fast: false
reversible: false
name: Pc phospholation
type: Reaction

metaid_0000051
is version of: GO:0044257
fast: false
reversible: false
name: Mp nonspecific degradation
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000083#bdcbc1e1_8470_4f87_96c6_db1992b928ec
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

metaid_0000021
boundary condition: false
initial concentration: 0.0
initial amount: NaN
name: PCcp
has part: O15534
in compartment: metaid_0000009
has only substance units: false
type: Species
has part: P56645
has part: Q8IV71
has part: Q16526
constant: false

http://identifiers.org/biomodels.db/BIOMD0000000083#_195dbb88_867d_4722_bc94_fa758be63e5a
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

536719
value: 0.1
name: Kdp
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000083#e8a4aa3b_25b0_4e88_a220_de9506f91c75
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000083#_1c59d95a_8c7c_4f5b_b6e2_49a4afd38a43
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

metaid_0000011
has version: O00327
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000009
name: Bc
type: Species

536670
value: 0.4
name: k2
type: LocalParameter

metaid_0000061
is version of: GO:0044257
fast: false
reversible: false
name: PCc nonspecific degradation
type: Reaction

536680
value: 0.02
name: kdmp
type: LocalParameter

metaid_0000071
is version of: GO:0006470
fast: false
reversible: false
name: Bnp dephospholation
type: Reaction

ORG:
  orgname: University of Oxford
n:
  given: Enuo
  family: He

W3 CDTF: Tue Jun 04 16:48:33 BST 2013