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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.
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species: metaid_0000012

metaid_0000088
type: Parameter
constant: false
value: NaN
name: LD

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

536646
type: LocalParameter
value: 1.006
name: Kp

536644
type: LocalParameter
value: 1.4
name: V1b

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

http://identifiers.org/biomodels.db/BIOMD0000000083#_6554e57c_2533_4c88_822a_5206d4720f7c
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000042
type: Reaction
is version of: GO:0043623
fast: false
reversible: true
name: Cc and Pc produce PCc

536664
type: LocalParameter
value: 0.4
name: k4

536663
type: LocalParameter
value: 0.8
name: k3

http://identifiers.org/biomodels.db/BIOMD0000000083#_83c6d7bb_8f69_4680_89e8_ed91a7dc438e
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

http://identifiers.org/biomodels.db/BIOMD0000000083#_263fe0e1_b964_4149_9bf9_27d15517c0d5
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

http://identifiers.org/biomodels.db/BIOMD0000000083#e5233c9f_3dad_4172_a328_e8d0f0946de4
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000057
type: Reaction
is version of: GO:0044257
fast: false
reversible: false
name: Cc nonspecific degradation

536691
type: LocalParameter
value: 0.02
name: kdnc

http://identifiers.org/biomodels.db/BIOMD0000000083#_17b7da5b_4de1_4b9e_8e1f_3c07dc2cb5f7
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

536695
type: LocalParameter
value: 0.02
name: kdn

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

metaid_0000089
type: Parameter
constant: false
value: NaN
name: vsp

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

536641
type: LocalParameter
value: 0.32
name: ksb

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

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

536660
type: LocalParameter
value: 0.3
name: Kd

536659
type: LocalParameter
value: 3.4
name: vdpc

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

metaid_0000047
type: Reaction
is version of: GO:0044257
fast: false
reversible: false
name: Bcp nonspecific degradation

536673
type: LocalParameter
value: 0.02
name: kdn

http://identifiers.org/biomodels.db/BIOMD0000000083#_1095c2f2_be97_4fec_a6e7_e0348f8989cb
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

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

536657
type: LocalParameter
value: 0.6
name: Kap

536656
type: LocalParameter
value: 2.0

http://identifiers.org/biomodels.db/BIOMD0000000083#_432c304a_8dab_4463_9d9a_f2c2d58c82cd
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

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

536662
type: LocalParameter
value: 1.006
name: Kp

536661
type: LocalParameter
value: 9.6
name: V1p

http://identifiers.org/biomodels.db/BIOMD0000000083#_84a02e41_6896_4c7a_b31a_2a6f2b59451c
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

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

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

536717
type: LocalParameter
value: 0.1
name: Kdp

536716
type: LocalParameter
value: 0.2
name: V2c

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

http://identifiers.org/biomodels.db/BIOMD0000000083#_18414da6_4c92_4ac3_baf8_e5f38553147f
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

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

536693
type: LocalParameter
value: 0.02
name: kdn

http://identifiers.org/biomodels.db/BIOMD0000000083#_972353ff_0fe9_45fc_9095_87ed87280f9a
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

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

536684
type: LocalParameter
value: 0.4
name: Kmb

536683
type: LocalParameter
value: 1.3
name: vmb

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

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

536731
type: LocalParameter
value: 1.7
name: ksr

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

metaid_0000046
type: Reaction
is version of: GO:0044257
fast: false
reversible: false
name: PCnp nonspecific degradation

536671
type: LocalParameter
value: 0.02
name: kdn

http://identifiers.org/biomodels.db/BIOMD0000000083#_33686406_75e3_4ad1_9099_df482eef7e4c
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

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

536735
type: LocalParameter
value: 0.4
name: k10

536733
type: LocalParameter
value: 0.8
name: k9

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

http://identifiers.org/biomodels.db/BIOMD0000000083#_55c9366d_112f_4baa_85e9_a6928076fdf7
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000078
type: Reaction
is version of: GO:0044257
fast: false
reversible: false
name: Mr nonspecific degradation

536728
type: LocalParameter
value: 0.02
name: kdmr

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

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

536649
type: LocalParameter
value: 3.2
name: ksc

http://identifiers.org/biomodels.db/BIOMD0000000083#c110d0ae_809b_4ee8_b31a_dbb7b24ebd66
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

536738
type: LocalParameter
value: 0.02
name: kdn

http://identifiers.org/biomodels.db/BIOMD0000000083#_0a9e52d4_5850_4288_9562_964640ab6fdb
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

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

536648
type: LocalParameter
value: 0.4
name: k6

536647
type: LocalParameter
value: 0.8
name: k5

http://identifiers.org/biomodels.db/BIOMD0000000083#b5273ae2_3221_46f5_8145_041ccc0894ef
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

http://identifiers.org/biomodels.db/BIOMD0000000083#f1859f6e_1f54_4b0f_9476_b2492734d492
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000054
type: Reaction
is version of: GO:0008233
fast: false
reversible: false
name: Mc specific degradation

536686
type: LocalParameter
value: 0.4
name: Kmc

536685
type: LocalParameter
value: 2.0
name: vmc

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

metaid_0000029
type: Reaction
is version of: GO:0045892
fast: false
reversible: false
name: Mb synthesized

536640
type: LocalParameter
value: 2.0
name: m

536638
type: LocalParameter
value: 1.0
name: Kib

536637
type: LocalParameter
value: 1.8
name: vsb

http://identifiers.org/biomodels.db/BIOMD0000000083#f7a81df6_7b6c_442d_a27b_0aab78505459
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

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

536724
type: LocalParameter
value: 0.1
name: Kdp

536723
type: LocalParameter
value: 0.2
name: V2pc

http://identifiers.org/biomodels.db/BIOMD0000000083#_68b9d59d_7565_4a85_88e3_34c34ce2a725
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

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

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

536674
type: LocalParameter
value: 0.02
name: kdn

http://identifiers.org/biomodels.db/BIOMD0000000083#b7133f67_0ec9_4e7c_993f_857cfc523bdf
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000049
type: Reaction
is part of: GO:0045893
fast: false
reversible: false
name: Mc synthesis

536677
type: LocalParameter
value: 0.6
name: Kac

536676
type: LocalParameter
value: 2.0

536675
type: LocalParameter
value: 2.2
name: vsc

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

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

536643
type: LocalParameter
value: 0.02
name: kdmb

http://identifiers.org/biomodels.db/BIOMD0000000083#_1a241c77_5fdd_4e27_a58b_9b72dc9901c1
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

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

536721
type: LocalParameter
value: 0.1
name: Kdp

536720
type: LocalParameter
value: 0.2
name: V4pc

http://identifiers.org/biomodels.db/BIOMD0000000083#d804af92_01ed_480b_99f3_06d00f0fcfa1
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

http://identifiers.org/biomodels.db/BIOMD0000000083#_16b8a7dc_5567_4671_baa3_41909d289815
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

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

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

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