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notes: This model is according to the paper Toward a detailed computational model for the mammalian circadian clock . In this model only interlocked negative and positive regulation of Per, Cry, Bmal gene are involved. Some initial values were not provided, therefore they were chosen to fit the curve from the paper. Figure2A re-produced by Copasi 4.0.19 and roadRunner online. 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.
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notes: Initial concentration for Mp got from the value of curve at time=0 in the paper.
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is version of: GO:0044257
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metaid_0000050
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metaid_0000010
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notes: The initial concentration of Mb got from the curve in the paper at time=0
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521267
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notes: In order to get the similar shape of the plot,we assigned 2nM as initial concentration for Bc
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is version of: GO:0045893
fast: false
reversible: false
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521800
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metaid_0000015
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notes: Initial concentration for Mc got from the value of the curve at time=0 in the paper.
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metaid_0000033
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is version of: GO:0006468
fast: false
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is version of: GO:0000060
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is version of: GO:0008233
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name: Mc specific degradation

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name: Kmc

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type: LocalParameter
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521982
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is version of: GO:0044257
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is version of: GO:0008233
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is version of: GO:0044257
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is version of: GO:0043623
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is version of: GO:0045892
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063934
type: LocalParameter
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is version of: GO:0044257
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522079
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is version of: GO:0044257
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064005
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522560
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is version of: GO:0044257
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521364
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metaid_0000053
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063968
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522030
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metaid_0000065
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063991
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063989
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522331
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is version of: GO:0008233
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is version of: GO:0008233
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value: 0.3
name: Kd

063980
type: LocalParameter
value: 0.5
name: vdbc

522223
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000067
type: Reaction
kinetic law: 522403
product: 522391
reactant: 522379
is version of: GO:0006470
fast: false
reversible: false
name: Bcp dephosphorylation

063996
type: LocalParameter
value: 0.1
name: Kdp

063994
type: LocalParameter
value: 0.1
name: V2b

522391
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

522379
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000027
type: Reaction
kinetic law: 521219
modifier: 521207
product: 521195
is version of: GO:0006412
fast: false
reversible: false
name: Mb translated into protein

063915
type: LocalParameter
value: 0.12
name: ksb

521195
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

521147
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000068
type: Reaction
kinetic law: 522439
product: 522427
reactant: 522415
is version of: GO:0006470
fast: false
reversible: false
name: Bnp dephosphorylation

063998
type: LocalParameter
value: 0.1
name: Kdp

063997
type: LocalParameter
value: 0.2
name: V4b

522427
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

522415
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

metaid_0000028
type: Reaction
kinetic law: 521243
reactant: 521231
is version of: GO:0044257
fast: false
reversible: false
name: Mb nonspecific degradation

063916
type: LocalParameter
value: 0.01
name: kdmb

521231
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000040
type: Reaction
kinetic law: 521653
product: 521641
reactant: 521629
is version of: GO:0006468
fast: false
reversible: false
name: PCc phosphorylation

063946
type: LocalParameter
value: 0.1
name: Kp

063945
type: LocalParameter
value: 0.4
name: V1pc

521641
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

521629
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

metaid_0000048
type: Reaction
kinetic law: 521891
reactant: 521878
is version of: GO:0044257
fast: false
reversible: false
name: Mp nonspecific degradation

063959
type: LocalParameter
value: 0.01
name: kdmp

521878
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

metaid_0000036
type: Reaction
kinetic law: 521508
modifier: 521496
product: 521484
is version of: GO:0006412
fast: false
reversible: false
name: Mp translated into protein

063938
type: LocalParameter
value: 0.6
name: ksp

521484
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

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

W3 CDTF: Tue Oct 17 16:43:58 BST 2006

W3 CDTF: Wed Jul 11 19:26:59 BST 2012