742041
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
type: Species

289929
value: 0.95
type: LocalParameter

289533
value: 3.2
type: LocalParameter

289353
stoichiometry: 1.0
species: 741921
type: SpeciesReference

289749
stoichiometry: 1.0
species: 742021
type: SpeciesReference

289833
stoichiometry: 1.0
species: 741942
type: SpeciesReference

742021
initial amount: NaN
constant: false
initial concentration: 0.25
type: Species
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

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

289437
stoichiometry: 1.0
species: 741921
type: SpeciesReference

289665
value: 2.0
type: LocalParameter

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

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

289893
stoichiometry: 1.0
species: 742001
type: SpeciesReference

289509
stoichiometry: 1.0
species: 741981
type: SpeciesReference

289485
value: 0.38
type: LocalParameter

742162
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
type: Reaction

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

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

289821
value: 1.3
type: LocalParameter

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

289401
value: 0.76
type: LocalParameter

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

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

289773
value: 1.9
type: LocalParameter

289629
stoichiometry: 1.0
species: 742001
type: SpeciesReference

289737
stoichiometry: 1.0
species: 742001
type: SpeciesReference

742142
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
type: Reaction

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

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

741921
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
type: Species

289449
stoichiometry: 1.0
species: 741962
type: SpeciesReference

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

289653
value: 5.0
type: LocalParameter

289869
value: 0.5
type: LocalParameter

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

741981
initial amount: NaN
type: Species
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

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

289569
stoichiometry: 1.0
species: 741962
type: SpeciesReference

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

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

289725
value: 2.0
type: LocalParameter

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

289785
stoichiometry: 1.0
species: 742021
type: SpeciesReference

289881
value: 0.65
type: LocalParameter

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

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

741962
constant: false
type: Species
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

289689
stoichiometry: 1.0
species: 741981
type: SpeciesReference

289905
stoichiometry: 1.0
species: 741921
type: SpeciesReference

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

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

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

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

289413
value: 1.0
type: LocalParameter

742102
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
type: Reaction

289605
value: 2.0
type: LocalParameter

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

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

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

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

742122
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
type: Reaction

289557
stoichiometry: 1.0
species: 741981
type: SpeciesReference

289797
stoichiometry: 1.0
species: 742001
type: SpeciesReference

289497
stoichiometry: 1.0
species: 741962
type: SpeciesReference

289713
value: 2.5
type: LocalParameter

289941
value: 0.2
type: LocalParameter

289677
stoichiometry: 1.0
species: 742001
type: SpeciesReference

289845
stoichiometry: 1.0
species: 741921
type: SpeciesReference

289425
value: 4.0
type: LocalParameter

289617
stoichiometry: 1.0
species: 741981
type: SpeciesReference

742001
has only substance units: false
constant: false
initial concentration: 0.25
initial amount: NaN
type: Species
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

289365
stoichiometry: 1.0
species: 741942
type: SpeciesReference

289545
value: 2.0
type: LocalParameter

289593
value: 1.58
type: LocalParameter