BIOMD0000000016
type: SBMLModel
species: 742001
time units: metaid_0000024
substance units: metaid_0000023
units def: metaid_0000024
species: 741942
reaction: 742182
notes: 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.
length unit: length
area units: area
species: 741981
reaction: 742222
occurs in: http://identifiers.org/taxonomy/7227
species: 741921
is version of: GO:0007623
creator:
  ORG:
    orgname: NASA Jet Propulsion Laboratory
  n:
    given: Bruce
    family: Shapiro
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Nicolas
    family: Le Novère
created:
  W3 CDTF: Wed Jun 29 11:17:21 BST 2005
reaction: 742162
compartment: metaid_0000026
is: dme04710
reaction: 742202
reaction: 742122
species: 741962
volume units: metaid_0000029
compartment: 741901
reaction: 742083
reaction: 742062
modified:
  W3 CDTF: Thu Jul 05 17:31:38 BST 2012
rule: metaid_0000025
reaction: 742142
species: 742041
name: Goldbeter1995_CircClock
units def: metaid_0000023
is described by: http://identifiers.org/pubmed/8587874
species: 742021
curated: true
is: MODEL6617161845
compartment: 741863
reaction: 742242
reaction: 742102

742001
type: Species
has only substance units: false
constant: false
initial concentration: 0.25
initial amount: NaN
is version of: P07663
boundary condition: false
notes: Initial condition changed from amount to concentration as per article. Bruce Shapiro
in compartment: 741901
name: biphosphorylated PER

741901
type: Compartment
is: GO:0005737
constant: true
size: 1.0E-15
spatial dimensions: 3.0

metaid_0000024
type: SBMLUnitsDef
unit: 289340
notes: Default unit of time redefined to hour by comparison with the article. Nicolas Le Novere
name: heure (default)

289340
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND

metaid_0000023
type: SBMLUnitsDef
unit: 289328
notes: Default unit of substance redefined to micromole by comparison with the article. Nicolas Le Novere
name: micromole (default)

289328
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

741942
type: Species
name: PER mRNA
has only substance units: false
initial amount: NaN
constant: false
is version of: C00046
is version of: CHEBI:33699
in compartment: 741901
boundary condition: false
notes: Initial condition changed from amount to concentration as per article. Bruce Shapiro
initial concentration: 0.1

742182
type: Reaction
kinetic law: 289761
product: 289749
reactant: 289737
is version of: GO:0006606
fast: false
reversible: false
name: translocation of PER to the nucleus

289761
type: KineticLaw
local parameters: 289773
notes: Formula modified to give units of substance/time Bruce Shapiro

289773
type: LocalParameter
value: 1.9

289749
type: SpeciesReference
stoichiometry: 1.0
species: 742021

742021
type: Species
initial amount: NaN
constant: false
initial concentration: 0.25
notes: Initial condition changed from amount to concentration as per article. Bruce Shapiro
boundary condition: false
is: P07663
name: nuclear PER
in compartment: metaid_0000026
has only substance units: false

metaid_0000026
type: Compartment
is: GO:0005634
constant: true
size: 1.0E-15
spatial dimensions: 3.0
name: NUCLEUS

289737
type: SpeciesReference
stoichiometry: 1.0
species: 742001

741981
type: Species
initial amount: NaN
boundary condition: false
has only substance units: false
notes: Initial condition changed from amount to concentration as per article. Bruce Shapiro
is version of: P07663
name: monophosphorylated PER
constant: false
in compartment: 741901
initial concentration: 0.25

742222
type: Reaction
kinetic law: 289857
product: 289845
reactant: 289833
is version of: GO:0006402
fast: false
reversible: false
name: degradation of PER mRNA

289857
type: KineticLaw
local parameters: 289881
local parameters: 289869
notes: Formula modified to give units of substance/time Bruce Shapiro

289881
type: LocalParameter
value: 0.65

289869
type: LocalParameter
value: 0.5

289845
type: SpeciesReference
stoichiometry: 1.0
species: 741921

741921
type: Species
notes: boundaryCondition changed from default (i.e. false) to true, because EmptySet acts as a reactant. Nicolas Le Novere
constant: true
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 741863

741863
type: Compartment
constant: true
size: 1.0E-15
spatial dimensions: 3.0

289833
type: SpeciesReference
stoichiometry: 1.0
species: 741942

742162
type: Reaction
kinetic law: 289701
product: 289689
reactant: 289677
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: removal of the second PER phosphate

289701
type: KineticLaw
local parameters: 289725
local parameters: 289713
notes: Formula modified to give units of substance/time Bruce Shapiro

289725
type: LocalParameter
value: 2.0

289713
type: LocalParameter
value: 2.5

289689
type: SpeciesReference
stoichiometry: 1.0
species: 741981

289677
type: SpeciesReference
stoichiometry: 1.0
species: 742001

742202
type: Reaction
kinetic law: 289809
product: 289797
reactant: 289785
is version of: GO:0006611
fast: false
reversible: false
name: translocation of PER to the cytoplasm

289809
type: KineticLaw
local parameters: 289821
notes: Formula modified to give units of substance/time Bruce Shapiro

289821
type: LocalParameter
value: 1.3

289797
type: SpeciesReference
stoichiometry: 1.0
species: 742001

289785
type: SpeciesReference
stoichiometry: 1.0
species: 742021

742122
type: Reaction
kinetic law: 289581
product: 289569
reactant: 289557
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: removal of the first PER phosphate

289581
type: KineticLaw
local parameters: 289605
local parameters: 289593
notes: Formula modified to give units of substance/time Bruce Shapiro

289605
type: LocalParameter
value: 2.0

289593
type: LocalParameter
value: 1.58

289569
type: SpeciesReference
stoichiometry: 1.0
species: 741962

741962
type: Species
constant: false
boundary condition: false
initial concentration: 0.25
is version of: P07663
name: unphosphorylated PER
notes: Initial condition changed from amount to concentration as per article. Bruce Shapiro
in compartment: 741901
initial amount: NaN
has only substance units: false

289557
type: SpeciesReference
stoichiometry: 1.0
species: 741981

742083
type: Reaction
kinetic law: 289473
modifier: 289461
product: 289449
reactant: 289437
is version of: GO:0006412
fast: false
reversible: false
name: translation of PER

289473
type: KineticLaw
local parameters: 289485
notes: Formula modified to give units of substance/time Bruce Shapiro

289485
type: LocalParameter
value: 0.38

289449
type: SpeciesReference
stoichiometry: 1.0
species: 741962

289437
type: SpeciesReference
stoichiometry: 1.0
species: 741921

742062
type: Reaction
is version of: GO:0009299
fast: false
name: transcription of PER
kinetic law: 289389
product: 289365
reversible: false
is version of: GO:0006355
reactant: 289353
modifier: 289377

289389
type: KineticLaw
local parameters: 289425
local parameters: 289413
local parameters: 289401
notes: Formula modified to give units of substance/time Bruce Shapiro

289425
type: LocalParameter
value: 4.0

289413
type: LocalParameter
value: 1.0

289401
type: LocalParameter
value: 0.76

289365
type: SpeciesReference
stoichiometry: 1.0
species: 741942

289353
type: SpeciesReference
stoichiometry: 1.0
species: 741921

metaid_0000025
notes: Conversion to number of molecules removed to give result in micromoles. Pn added to formula for consistency with reference. Bruce Shapiro

742142
type: Reaction
kinetic law: 289641
product: 289629
reactant: 289617
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 PER

289641
type: KineticLaw
local parameters: 289665
local parameters: 289653
notes: Formula modified to give units of substance/time Bruce Shapiro

289665
type: LocalParameter
value: 2.0

289653
type: LocalParameter
value: 5.0

289629
type: SpeciesReference
stoichiometry: 1.0
species: 742001

289617
type: SpeciesReference
stoichiometry: 1.0
species: 741981

742041
type: Species
initial amount: NaN
boundary condition: false
is: P07663
initial concentration: 1.0
name: total PER
constant: false
notes: Initial condition changed from amount to concentration as per article. Bruce Shapiro initial concentration for Pt is not used becuase Pt is determined by an Assigment Rule
has only substance units: false
in compartment: 741901

742242
type: Reaction
kinetic law: 289917
product: 289905
reactant: 289893
is version of: GO:0006402
fast: false
reversible: false
name: degradation of PER

289917
type: KineticLaw
local parameters: 289941
local parameters: 289929
notes: Formula modified to give units of substance/time Bruce Shapiro

289941
type: LocalParameter
value: 0.2

289929
type: LocalParameter
value: 0.95

289905
type: SpeciesReference
stoichiometry: 1.0
species: 741921

289893
type: SpeciesReference
stoichiometry: 1.0
species: 742001

742102
type: Reaction
kinetic law: 289521
product: 289509
reactant: 289497
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 PER

289521
type: KineticLaw
local parameters: 289545
local parameters: 289533
notes: Formula modified to give units of substance/time Bruce Shapiro

289545
type: LocalParameter
value: 2.0

289533
type: LocalParameter
value: 3.2

289509
type: SpeciesReference
stoichiometry: 1.0
species: 741981

289497
type: SpeciesReference
stoichiometry: 1.0
species: 741962