727279
value: 0.2
type: LocalParameter

727309
value: 0.2
type: LocalParameter

727239
value: 2.0
type: LocalParameter

metaid_0000045
kinetic law: 937327
modifier: 937315
product: 937303
is version of: GO:0006412
fast: false
reversible: false
name: PER production
type: Reaction

727294
value: 0.01
type: LocalParameter

727269
value: 1.0
type: LocalParameter

metaid_0000038
kinetic law: 937086
reactant: 937074
is version of: GO:0030163
fast: false
reversible: false
name: TIM-2 degradation
type: Reaction

727261
value: 8.0
type: LocalParameter

727301
value: 4.0
type: LocalParameter

metaid_0000031
kinetic law: 936905
product: 936893
reactant: 936881
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: Dephosphorylation of PER (2nd P)
type: Reaction

metaid_0000003
unit: 936637
name: nanomole (default)
type: SBMLUnitsDef

727289
value: 0.6
type: LocalParameter

metaid_0000013
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000012
name: PER Protein (unphosphorylated)
type: Species

727299
value: 1.0
type: LocalParameter

936747
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000025
name: First Phosphorylation of PER
is version of: http://identifiers.org/ec-code/2.7.11.1
is version of: GO:0006468
product: 936673
fast: false
type: Reaction
notes: This phosphorylation is triggered by the protein product of the gene double-time (DBT, DCO_DROME ). Not explicitely represented in the model.
kinetic law: 936686
reversible: false
reactant: 936661

937098
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

727293
value: 0.01
type: LocalParameter

metaid_0000044
kinetic law: 937291
modifier: 937279
product: 937267
is version of: GO:0006355
is version of: GO:0009299
fast: false
reversible: false
name: TIM mRNA production
type: Reaction

936808
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000039
kinetic law: 937134
product: 937122
reactant: 937110
reactant: 937098
is version of: GO:0006461
fast: false
reversible: true
name: PER-TIM complex formation
type: Reaction

727257
value: 8.0
type: LocalParameter

937303
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000030
kinetic law: 936869
product: 936857
reactant: 936845
is version of: GO:0006468
is version of: http://identifiers.org/ec-code/2.7.11.1
fast: false
reversible: false
name: Second Phosphorylation of TIM
type: Reaction

936845
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

727273
value: 0.01
type: LocalParameter

metaid_0000012
is: GO:0005737
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

727243
value: 2.0
type: LocalParameter

727283
value: 0.2
type: LocalParameter

937122
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

936953
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000026
kinetic law: 936723
product: 936711
reactant: 936699
is version of: GO:0006468
is version of: http://identifiers.org/ec-code/2.7.11.1
fast: false
reversible: false
name: First Phosphorylation of TIM
type: Reaction

727303
value: 0.9
type: LocalParameter

metaid_0000036
kinetic law: 937037
reactant: 937025
is version of: GO:0030163
fast: false
reversible: false
name: TIM-1 degradation
type: Reaction

727267
value: 2.0
type: LocalParameter

937049
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000047
kinetic law: 937388
reactant: 937376
is version of: GO:0006402
fast: false
reversible: false
name: PER mRNA degradation
type: Reaction

727272
value: 0.01
type: LocalParameter

727287
value: 0.6
type: LocalParameter

936735
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

727304
value: 0.9
type: LocalParameter

metaid_0000009
constant: false
value: NaN
name: Total Tim
type: Parameter

metaid_0000015
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000012
name: PER Protein (mono-phosphorylated)
type: Species

metaid_0000027
kinetic law: 936759
product: 936747
reactant: 936735
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: Dephosphorylation of PER (1st P)
type: Reaction

metaid_0000037
kinetic law: 937062
reactant: 937049
is version of: GO:0030163
fast: false
reversible: false
name: PER-2 degradation
type: Reaction

727291
value: 0.2
type: LocalParameter

metaid_0000046
kinetic law: 937364
modifier: 937352
product: 937340
is version of: GO:0006412
fast: false
reversible: false
name: TIM production
type: Reaction

937001
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

727255
value: 2.0
type: LocalParameter

727285
value: 1.2
type: LocalParameter

727271
value: 0.01
type: LocalParameter

metaid_0000014
is version of: P49021
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000012
name: TIM Protein (unphosphorylated)
type: Species

727245
value: 8.0
type: LocalParameter

936857
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

metaid_0000008
constant: false
value: NaN
name: Total Per
type: Parameter

937182
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

937267
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

727265
value: 1.0
type: LocalParameter

metaid_0000028
kinetic law: 936796
product: 936783
reactant: 936771
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: Dephosphorylation of TIM (1st P)
type: Reaction

937230
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

937146
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

727298
value: 1.0
type: LocalParameter

metaid_0000041
kinetic law: 937194
reactant: 937182
is version of: GO:0030163
fast: false
reversible: false
name: PER-TIM complex degradation (cytosol)
type: Reaction

727305
value: 0.01
type: LocalParameter

727275
value: 0.01
type: LocalParameter

metaid_0000048
kinetic law: 937412
reactant: 937400
is version of: GO:0006402
fast: false
reversible: false
name: TIM mRNA degradation
type: Reaction

metaid_0000035
kinetic law: 937013
reactant: 937001
is version of: GO:0030163
fast: false
reversible: false
name: PER-1 degradation
type: Reaction

metaid_0000017
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000012
name: PER Protein (bi-phosphorylated)
type: Species

937074
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

936881
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

727249
value: 1.0
type: LocalParameter

metaid_0000021
name: PER mRNA
in compartment: metaid_0000012
is version of: CHEBI:33699
boundary condition: false
has only substance units: false
initial amount: NaN
type: Species
is version of: C00046
constant: false
initial concentration: 0.0

936661
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

936649
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND
type: SBMLUnit

727247
value: 2.0
type: LocalParameter

936637
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000040
kinetic law: 937170
product: 937158
reactant: 937146
is version of: GO:0006606
fast: false
reversible: true
name: PER-TIM complex nucleation
type: Reaction

727297
value: 4.0
type: LocalParameter

727276
value: 0.01
type: LocalParameter

727306
value: 0.7
type: LocalParameter

936783
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000049
is: GO:0005634
constant: true
size: 1.0
spatial dimensions: 3.0
name: nucleus
type: Compartment

937206
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000029
is version of: GO:0006468
fast: false
name: Second Phosphorylation of PER
type: Reaction
reversible: false
notes: This phosphorylation is triggered by the protein product of the gene double-time (DBT, DCO_DROME ). Not explicitely represented in the model.
product: 936820
kinetic law: 936833
is version of: http://identifiers.org/ec-code/2.7.11.1
reactant: 936808

metaid_0000016
is version of: P49021
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000012
name: TIM Protein (mono-phosphorylated)
type: Species

BIOMD0000000021
species: metaid_0000019
parameter: metaid_0000008
parameter: metaid_0000009
reaction: metaid_0000046
reaction: metaid_0000047
reaction: metaid_0000028
reaction: metaid_0000042
compartment: metaid_0000012
time units: metaid_0000005
species: metaid_0000020
units def: metaid_0000003
volume units: metaid_0000323
is described by: http://identifiers.org/pubmed/10366496
is derived from: BIOMD0000000171
reaction: metaid_0000037
species: metaid_0000014
parameter: metaid_0000010
reaction: metaid_0000038
length unit: length
species: metaid_0000017
curated: true
reaction: metaid_0000044
reaction: metaid_0000045
reaction: metaid_0000035
reaction: metaid_0000040
reaction: metaid_0000041
reaction: metaid_0000031
is: MODEL6617834203
occurs in: http://identifiers.org/taxonomy/7227
is: dme04710
is version of: GO:0007623
modified:
  W3 CDTF: Tue May 15 22:38:35 BST 2012
creator:
  ORG:
    orgname: NASA Jet Propulsion Laboratory
  n:
    given: Bruce
    family: Shapiro
compartment: metaid_0000049
species: metaid_0000021
reaction: metaid_0000036
reaction: metaid_0000026
reaction: metaid_0000027
created:
  W3 CDTF: Wed Jun 29 11:27:52 BST 2005
notes: This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
species: metaid_0000015
reaction: metaid_0000033
units def: metaid_0000005
reaction: metaid_0000034
species: metaid_0000018
reaction: metaid_0000030
substance units: metaid_0000003
name: Leloup1999_CircClock
reaction: metaid_0000029
species: metaid_0000022
rule: metaid_0000023
reaction: metaid_0000043
type: SBMLModel
reaction: metaid_0000025
species: metaid_0000013
rule: metaid_0000024
reaction: metaid_0000048
area units: area
reaction: metaid_0000039
reaction: metaid_0000032
parameter: metaid_0000011
species: metaid_0000016
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Nicolas
    family: Le Novère

936917
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

metaid_0000020
boundary condition: false
in compartment: metaid_0000049
initial concentration: 0.0
constant: false
type: Species
has part: P07663
initial amount: NaN
has only substance units: false
has part: P49021
name: Nuclear PER-TIM Complex

metaid_0000034
kinetic law: 936989
reactant: 936977
is version of: GO:0030163
fast: false
reversible: false
name: TIM degradation
type: Reaction

727253
value: 1.0
type: LocalParameter

936699
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

936820
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000010
notes: V_mT=.7 (physiological oscillations); 0.28 (chaos); .4 or .99 (biorhythmicity example)
constant: true
value: 0.7
type: Parameter

937158
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

metaid_0000043
kinetic law: 937254
modifier: 937242
product: 937230
is version of: GO:0006355
is version of: GO:0009299
fast: false
reversible: false
name: PER mRNA production
type: Reaction

727263
value: 2.0
type: LocalParameter

727307
value: 0.2
type: LocalParameter

727277
value: 2.0
type: LocalParameter

727296
value: 1.0
type: LocalParameter

metaid_0000019
initial concentration: 0.0
has part: P49021
in compartment: metaid_0000012
has part: P07663
boundary condition: false
type: Species
constant: false
name: Cytosolic PER-TIM Complex
initial amount: NaN
has only substance units: false

937400
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

metaid_0000033
kinetic law: 936965
reactant: 936953
is version of: GO:0030163
fast: false
reversible: false
name: PER degradation
type: Reaction

936977
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

936673
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

937376
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

metaid_0000005
unit: 936649
name: hour (default)
type: SBMLUnitsDef

937025
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

937340
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

936893
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000011
notes: V_dT=2 (physiological oscillations); 4.8 (chaos); 3.8 or 2 (biorhythmicity example)
constant: true
value: 2.0
type: Parameter

936711
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

937110
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

727295
value: 1.0
type: LocalParameter

metaid_0000042
kinetic law: 937218
reactant: 937206
is version of: GO:0030163
fast: false
reversible: false
name: PER-TIM complex degradation (nuclear)
type: Reaction

metaid_0000018
is version of: P49021
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000012
name: TIM Protein (bi-phosphorylated)
type: Species

727308
value: 0.01
type: LocalParameter

727259
value: 2.0
type: LocalParameter

metaid_0000032
kinetic law: 936941
product: 936929
reactant: 936917
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: Dephosphorylation of TIM (2nd P)
type: Reaction

727281
value: 0.01
type: LocalParameter

727241
value: 8.0
type: LocalParameter

727251
value: 2.0
type: LocalParameter

936771
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000022
initial concentration: 0.0
name: TIM mRNA
initial amount: NaN
has only substance units: false
in compartment: metaid_0000012
is version of: C00046
is version of: CHEBI:33699
type: Species
constant: false
boundary condition: false

936929
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference