BIOMD0000000021
type: SBMLModel
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
creator:
  ORG:
    orgname: NASA Jet Propulsion Laboratory
  n:
    given: Bruce
    family: Shapiro
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
compartment: metaid_0000049
species: metaid_0000021
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Nicolas
    family: Le Novère
reaction: metaid_0000036
reaction: metaid_0000026
reaction: metaid_0000027
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.
modified:
  W3 CDTF: Tue May 15 22:38:35 BST 2012
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
reaction: metaid_0000025
species: metaid_0000013
created:
  W3 CDTF: Wed Jun 29 11:27:52 BST 2005
rule: metaid_0000024
reaction: metaid_0000048
area units: area
reaction: metaid_0000039
reaction: metaid_0000032
parameter: metaid_0000011
species: metaid_0000016

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

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

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

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

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

727304
type: LocalParameter
value: 0.9

metaid_0000022
type: Species
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
constant: false
boundary condition: false

937340
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000014
type: Species
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)

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

727307
type: LocalParameter
value: 0.2

727306
type: LocalParameter
value: 0.7

727305
type: LocalParameter
value: 0.01

937376
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

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

metaid_0000028
type: Reaction
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)

727253
type: LocalParameter
value: 1.0

727251
type: LocalParameter
value: 2.0

936783
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

936771
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000016
type: Species
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)

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

727294
type: LocalParameter
value: 0.01

937206
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

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

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

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

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

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

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

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

727279
type: LocalParameter
value: 0.2

727277
type: LocalParameter
value: 2.0

727276
type: LocalParameter
value: 0.01

937049
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

metaid_0000017
type: Species
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)

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

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

727283
type: LocalParameter
value: 0.2

727281
type: LocalParameter
value: 0.01

937074
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

metaid_0000018
type: Species
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)

metaid_0000044
type: Reaction
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

727301
type: LocalParameter
value: 4.0

727299
type: LocalParameter
value: 1.0

727298
type: LocalParameter
value: 1.0

937267
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

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

727303
type: LocalParameter
value: 0.9

937303
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

metaid_0000013
type: Species
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)

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

727273
type: LocalParameter
value: 0.01

937001
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

metaid_0000015
type: Species
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)

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

727291
type: LocalParameter
value: 0.2

727289
type: LocalParameter
value: 0.6

937158
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

937146
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

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

727293
type: LocalParameter
value: 0.01

937182
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

metaid_0000031
type: Reaction
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)

727265
type: LocalParameter
value: 1.0

727263
type: LocalParameter
value: 2.0

936893
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

936881
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

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

727275
type: LocalParameter
value: 0.01

937025
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000026
type: Reaction
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

727245
type: LocalParameter
value: 8.0

727243
type: LocalParameter
value: 2.0

936711
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

936699
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000027
type: Reaction
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)

727249
type: LocalParameter
value: 1.0

727247
type: LocalParameter
value: 2.0

936747
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

936735
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

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

727271
type: LocalParameter
value: 0.01

936953
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

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

727272
type: LocalParameter
value: 0.01

936977
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000030
type: Reaction
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

727261
type: LocalParameter
value: 8.0

727259
type: LocalParameter
value: 2.0

936857
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

936845
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000029
type: Reaction
is version of: GO:0006468
fast: false
name: Second Phosphorylation of PER
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

936820
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

727257
type: LocalParameter
value: 8.0

727255
type: LocalParameter
value: 2.0

936808
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

metaid_0000043
type: Reaction
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

727297
type: LocalParameter
value: 4.0

727296
type: LocalParameter
value: 1.0

727295
type: LocalParameter
value: 1.0

937230
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

metaid_0000025
type: Reaction
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
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

936673
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

727241
type: LocalParameter
value: 8.0

727239
type: LocalParameter
value: 2.0

936661
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

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

727309
type: LocalParameter
value: 0.2

727308
type: LocalParameter
value: 0.01

937400
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

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

727287
type: LocalParameter
value: 0.6

727285
type: LocalParameter
value: 1.2

937122
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

937110
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

937098
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

metaid_0000032
type: Reaction
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)

727269
type: LocalParameter
value: 1.0

727267
type: LocalParameter
value: 2.0

936929
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

936917
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

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