BIOMD0000000170
type: SBMLModel
species: metaid_0000034
reaction: metaid_0000051
reaction: metaid_0000050
reaction: metaid_0000047
reaction: metaid_0000057
reaction: metaid_0000048
units def: metaid_0000062
area units: metaid_0000005
parameter: metaid_0000020
parameter: metaid_0000029
substance units: metaid_0000061
occurs in: http://identifiers.org/taxonomy/40674
units def: metaid_0000064
rule: metaid_0000041
parameter: metaid_0000027
time units: metaid_0000062
rule: metaid_0000043
species: metaid_0000035
reaction: metaid_0000055
parameter: metaid_0000023
parameter: metaid_0000006
reaction: metaid_0000054
compartment: metaid_0000030
species: metaid_0000033
is described by: http://identifiers.org/pubmed/15347590
curated: true
parameter: metaid_0000003
parameter: metaid_0000013
compartment: metaid_0000031
parameter: metaid_0000004
reaction: metaid_0000052
reaction: metaid_0000049
reaction: metaid_0000059
is part of: hsa04710
reaction: metaid_0000045
species: metaid_0000038
reaction: metaid_0000058
notes: The model reproduces the time profile of the species as depicted in Fig 3A of the paper. Model successfully tested on MathSBML and Jarnac.
rule: metaid_0000042
units def: metaid_0000063
parameter: metaid_0000007
parameter: metaid_0000017
parameter: metaid_0000008
reaction: metaid_0000056
units def: metaid_0000065
parameter: metaid_0000005
parameter: metaid_0000015
species: metaid_0000039
parameter: metaid_0000011
is: GO:0007623
parameter: metaid_0000014
parameter: metaid_0000024
modified:
  W3 CDTF: Wed May 16 11:04:56 BST 2012
reaction: metaid_0000060
parameter: metaid_0000010
species: metaid_0000037
length unit: length
is: MODEL8378813456
created:
  W3 CDTF: Wed Apr 16 12:56:13 BST 2008
units def: metaid_0000061
parameter: metaid_0000009
parameter: metaid_0000019
reaction: metaid_0000046
name: Weimann2004_CircadianOscillator
parameter: metaid_0000018
parameter: metaid_0000028
units def: metaid_0000066
parameter: metaid_0000025
species: metaid_0000036
reaction: metaid_0000053
parameter: metaid_0000021
volume units: metaid_0000004
parameter: metaid_0000016
parameter: metaid_0000026
reaction: metaid_0000044
creator:
  ORG:
    orgname: California Institute of Technology
  n:
    given: Harish
    family: Dharuri
parameter: metaid_0000012
parameter: metaid_0000022

metaid_0000034
type: Species
initial concentration: 0.0
boundary condition: false
name: PER2_CRY_complex_cytoplasm
constant: false
initial amount: NaN
in compartment: metaid_0000031
has part: O15055
has part: Q16526
has only substance units: false

metaid_0000031
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: Cytoplasm

metaid_0000051
type: Reaction
kinetic law: 748880
product: 748868
is version of: GO:0006351
fast: false
reversible: false
name: Bmal1_transcription

748868
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

metaid_0000036
type: Species
is version of: CHEBI:33699
in compartment: metaid_0000031
is version of: C00046
initial amount: NaN
encodes: Q8IUT4
constant: false
has only substance units: false
boundary condition: false
name: Bmal1 mRNA
initial concentration: 0.8

metaid_0000050
type: Reaction
kinetic law: 748856
reactant: 748844
is version of: GO:0044257
fast: false
reversible: false
name: nuclear_per2_cry_complex_degradation

748844
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000035

metaid_0000035
type: Species
name: PER2_CRY_complex_nucleus
has part: Q16526
boundary condition: false
in compartment: metaid_0000030
initial concentration: 1.1
initial amount: NaN
has part: O15055
constant: false
has only substance units: false

metaid_0000030
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: Nucleus

metaid_0000047
type: Reaction
kinetic law: 748759
reactant: 748747
is version of: GO:0044257
fast: false
reversible: false
name: cytoplasmic_per2_cry_complex_degradation

748747
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

metaid_0000057
type: Reaction
kinetic law: 749062
reactant: 749049
is version of: GO:0044257
fast: false
reversible: false
name: nuclear_BMAL1_degradation

749049
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

metaid_0000038
type: Species
is version of: Q8IUT4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: metaid_0000030
name: BMAL1_nucleus

metaid_0000048
type: Reaction
kinetic law: 748796
product: 748784
reactant: 748771
is version of: GO:0051170
fast: false
reversible: false
name: per2_cry_nuclear_import

748784
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000035

748771
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

metaid_0000062
type: SBMLUnitsDef
unit: 748540
name: hour

748540
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND

metaid_0000020
type: Parameter
constant: true
units: metaid_0000065
value: 0.12

metaid_0000065
type: SBMLUnitsDef
unit: 748613
name: hr_inv

748613
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND

metaid_0000029
type: Parameter
constant: true
units: metaid_0000065
value: 0.09

metaid_0000061
type: SBMLUnitsDef
unit: 748528
name: nano mole

748528
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000064
type: SBMLUnitsDef
unit: 748601
unit: 748589
unit: 748577
name: nM_per_hour

748601
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND

748589
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

748577
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000027
type: Parameter
constant: true
units: metaid_0000065
value: 0.09

metaid_0000055
type: Reaction
kinetic law: 749001
product: 748988
reactant: 748976
is version of: GO:0051170
fast: false
reversible: false
name: BMAL1_nuclear_import

748988
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

748976
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

metaid_0000037
type: Species
is version of: Q8IUT4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: metaid_0000031
name: BMAL1_cytoplasm

metaid_0000023
type: Parameter
constant: true
units: metaid_0000065
value: 0.06

metaid_0000006
type: Parameter
constant: true
units: metaid_0000063
value: 1.0

metaid_0000063
type: SBMLUnitsDef
unit: 748564
unit: 748552
name: nM

748564
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

748552
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000054
type: Reaction
kinetic law: 748964
reactant: 748952
is version of: GO:0044257
fast: false
reversible: false
name: cytoplasmic_BMAL1_degradation

748952
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

metaid_0000033
type: Species
name: Per2 or Cry mRNA
in compartment: metaid_0000031
has only substance units: false
constant: false
initial amount: NaN
encodes: Q16526
is version of: C00046
encodes: O15055
is version of: CHEBI:33699
initial concentration: 0.2
boundary condition: false

metaid_0000003
type: Parameter
constant: false
units: metaid_0000064
value: 0.0

metaid_0000013
type: Parameter
constant: false
units: metaid_0000063
value: 3.05

metaid_0000004
type: Parameter
constant: true
units: metaid_0000064
value: 9.0

metaid_0000052
type: Reaction
kinetic law: 748904
reactant: 748892
is version of: GO:0006402
fast: false
reversible: false
name: Bmal1_mRNA_degradation

748892
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

metaid_0000049
type: Reaction
kinetic law: 748832
product: 748820
reactant: 748808
is version of: GO:0051168
fast: false
reversible: false
name: per2_cry_nuclear_export

748820
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

748808
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000035

metaid_0000059
type: Reaction
kinetic law: 749134
product: 749122
reactant: 749110
is version of: GO:0043433
fast: false
reversible: false
name: BMAL1_deactivation

749122
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

749110
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

metaid_0000039
type: Species
is version of: Q8IUT4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.05
initial amount: NaN
in compartment: metaid_0000030
name: Active BMAL1

metaid_0000045
type: Reaction
kinetic law: 748698
reactant: 748686
is version of: GO:0006402
fast: false
reversible: false
name: per2_cry_mRNA_degradation

748686
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

metaid_0000058
type: Reaction
kinetic law: 749098
product: 749086
reactant: 749074
is version of: GO:0051091
fast: false
reversible: false
name: BMAL1_activation

749086
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

749074
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

metaid_0000007
type: Parameter
constant: true
units: metaid_0000063
value: 0.56

metaid_0000017
type: Parameter
constant: true
units: metaid_0000065
value: 0.05

metaid_0000008
type: Parameter
constant: true
units: dimensionless
value: 8.0

metaid_0000056
type: Reaction
kinetic law: 749037
product: 749025
reactant: 749013
is version of: GO:0051168
fast: false
reversible: false
name: BMAL1_nuclear_export

749025
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

749013
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

metaid_0000005
type: Parameter
constant: true
units: metaid_0000063
value: 0.01

metaid_0000015
type: Parameter
constant: true
units: metaid_0000066
value: 0.3

metaid_0000066
type: SBMLUnitsDef
unit: 748650
unit: 748638
unit: 748625
name: nM_inv_hr_inv

748650
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 3600.0
kind: SECOND

748638
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

748625
type: SBMLUnit
exponent: -1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000011
type: Parameter
constant: true
units: dimensionless
value: 3.0

metaid_0000014
type: Parameter
constant: true
units: metaid_0000065
value: 0.12

metaid_0000024
type: Parameter
constant: true
units: metaid_0000065
value: 0.45

metaid_0000060
type: Reaction
kinetic law: 749159
reactant: 749146
is version of: GO:0044257
fast: false
reversible: false
name: Active_BMAL1_degradation

749146
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000039

metaid_0000010
type: Parameter
constant: true
units: metaid_0000064
value: 3.6

metaid_0000009
type: Parameter
constant: false
units: metaid_0000064
value: 0.0

metaid_0000019
type: Parameter
constant: true
units: metaid_0000065
value: 0.02

metaid_0000046
type: Reaction
kinetic law: 748734
modifier: 748722
product: 748710
is version of: GO:0046982
fast: false
reversible: false
name: per2_cry_complex_formation

748710
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

metaid_0000018
type: Parameter
constant: true
units: metaid_0000065
value: 0.24

metaid_0000028
type: Parameter
constant: true
units: metaid_0000065
value: 0.003

metaid_0000025
type: Parameter
constant: true
units: metaid_0000065
value: 0.06

metaid_0000053
type: Reaction
kinetic law: 748940
modifier: 748928
product: 748916
is version of: GO:0006412
fast: false
reversible: false
name: BMAL1_translation

748916
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

metaid_0000021
type: Parameter
constant: true
units: metaid_0000065
value: 0.75

metaid_0000016
type: Parameter
constant: true
units: dimensionless
value: 2.0

metaid_0000026
type: Parameter
constant: true
units: metaid_0000065
value: 0.12

metaid_0000044
type: Reaction
kinetic law: 748674
product: 748662
is version of: GO:0006351
fast: false
reversible: false
name: per2_cry_transcription

748662
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

metaid_0000012
type: Parameter
constant: true
units: metaid_0000063
value: 2.16

metaid_0000022
type: Parameter
constant: true
units: metaid_0000065
value: 0.24