294194
units: metaid_0000022
value: 2.0
name: P1_kinase_KM
type: LocalParameter

222299
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000048
reversible: false
kinetic law: 222774
fast: false
reactant: 222748
is version of: R00162
type: Reaction
name: TIM-p phosphorylation
is version of: GO:0006468
product: 222761
is version of: http://identifiers.org/ec-code/2.7.11.1

222683
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

294216
units: metaid_0000022
value: 0.2
name: P2_light_deactivation_KM
type: LocalParameter

metaid_0000013
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.02
initial amount: NaN
in compartment: metaid_0000052
name: PER
type: Species

222395
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

222605
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

294189
units: metaid_0000023
value: 8.0
name: P0_phos_rate
type: LocalParameter

metaid_0000020
unit: 221925
name: nanomolar
type: SBMLUnitsDef

metaid_0000007
boundary condition: false
name: per mRNA
constant: false
initial amount: NaN
initial concentration: 0.09
is version of: C02100
has only substance units: false
type: Species
is version of: CHEBI:33699
in compartment: metaid_0000052

metaid_0000034
kinetic law: 222335
reactant: 222323
is version of: GO:0030163
fast: false
reversible: false
name: PER-pp decay
type: Reaction

222567
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

222839
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

222071
exponent: -1.0
scale: 3
multipler: 3.6
kind: SECOND
type: SBMLUnit

221951
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

metaid_0000053
kinetic law: 222878
reactant: 222865
is version of: GO:0030163
fast: false
reversible: false
name: TIM-pp light deactivation
type: Reaction

metaid_0000027
constant: true
units: metaid_0000028
value: 0.01
name: degradation_rate
type: Parameter

222644
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

294203
units: metaid_0000022
value: 2.0
name: T0_kinase_KM
type: LocalParameter

222023
exponent: -1.0
scale: 3
multipler: 3.6
kind: SECOND
type: SBMLUnit

metaid_0000047
type: Reaction
is version of: GO:0006468
is version of: http://identifiers.org/ec-code/2.7.11.1
reactant: 222709
kinetic law: 222735
product: 222722
name: TIM phosphorylation
reversible: false
is version of: R00162
fast: false

222443
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000040
kinetic law: 222479
reactant: 222467
is version of: GO:0030163
fast: false
reversible: false
name: cytopl. PER_TIM compl. decay
type: Reaction

294161
units: metaid_0000063
value: 0.8
name: per_max_transkr_rate
type: LocalParameter

metaid_0000060
constant: false
units: metaid_0000023
value: 2.0
name: T2_lightdecay_rate
type: Parameter

294182
units: metaid_0000028
value: 0.01
name: CN_decay_rate
type: LocalParameter

metaid_0000008
is version of: P49021
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.54
initial amount: NaN
in compartment: metaid_0000052
name: TIM
type: Species

metaid_0000014
initial concentration: 0.02
constant: false
has only substance units: false
boundary condition: false
is version of: C00562
in compartment: metaid_0000052
type: Species
is version of: P07663
initial amount: NaN
name: PER-p

metaid_0000033
kinetic law: 222311
reactant: 222299
is version of: GO:0030163
fast: false
reversible: false
name: PER-p decay
type: Reaction

metaid_0000054
kinetic law: 222904
reactant: 222891
is version of: GO:0030163
fast: false
reversible: false
name: PER-pp light deactivation
type: Reaction

221938
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

294192
units: metaid_0000023
value: 8.0
name: P1_phosph_rate
type: LocalParameter

metaid_0000028
unit: 222011
name: perhour
type: SBMLUnitsDef

294204
units: metaid_0000023
value: 8.0
name: T1_phosph_rate
type: LocalParameter

294197
units: metaid_0000023
value: 1.0
name: P1_dephos_rate
type: LocalParameter

222709
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

222059
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

294164
units: metaid_0000022
value: 1.0
name: per_inh_konstant
type: LocalParameter

294214
units: metaid_0000023
value: 2.0
name: P2_light_deactivation_rate
type: LocalParameter

metaid_0000036
kinetic law: 222383
reactant: 222371
is version of: GO:0030163
fast: false
reversible: false
name: TIM-p decay
type: Reaction

221963
exponent: 1.0
scale: 3
multipler: 3.6
kind: SECOND
type: SBMLUnit

222800
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

222083
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

metaid_0000015
is version of: C00562
boundary condition: false
type: Species
initial concentration: 0.01
name: PER-pp
initial amount: NaN
in compartment: metaid_0000052
constant: false
has only substance units: false
is version of: P07663

294181
units: metaid_0000028
value: 0.01
name: C_decay_rate
type: LocalParameter

222011
exponent: -1.0
scale: 3
multipler: 3.6
kind: SECOND
type: SBMLUnit

222491
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000046
kinetic law: 222696
product: 222683
reactant: 222670
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: PER-pp dephosphorylation
type: Reaction

222670
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000055
has version: P49021
constant: false
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid_0000052
name: total TIM
type: Species

222347
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

294198
units: metaid_0000023
value: 1.0
name: P2_dephos_rate
type: LocalParameter

222179
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

294195
units: metaid_0000022
value: 2.0
name: P1_phosphatase_KM
type: LocalParameter

222865
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

222431
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

222419
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000066
constant: true
units: metaid_0000023
value: 2.0
name: v_dT_value_darkness
type: Parameter

metaid_0000035
kinetic law: 222359
reactant: 222347
is version of: GO:0030163
fast: false
reversible: false
name: TIM decay
type: Reaction

222631
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000006
constant: false
is version of: CHEBI:33699
type: Species
initial concentration: 1.41
is version of: C02100
initial amount: NaN
in compartment: metaid_0000052
name: tim mRNA
has only substance units: false
boundary condition: false

metaid_0000016
name: PER_TIM complex cytoplasm
boundary condition: false
has only substance units: false
is version of: GO:0043234
has part: P49021
initial concentration: 0.18
type: Species
in compartment: metaid_0000052
initial amount: NaN
has part: P07663
constant: false

294180
units: metaid_0000028
value: 0.6
name: C_diss_rate
type: LocalParameter

221999
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

294178
units: metaid_0000039
value: 1.2
name: T_P_ass_rate
type: LocalParameter

222371
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000026
kinetic law: 222167
reactant: 222155
is version of: GO:0006402
fast: false
reversible: false
name: tim mRNA decay
type: Reaction

metaid_0000056
constant: true
units: metaid_0000021
value: 12.0
name: light_dark_period
type: Parameter

metaid_0000045
kinetic law: 222657
product: 222644
reactant: 222631
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: PER-p dephosphorylation
type: Reaction

metaid_0000038
reversible: false
name: Per_TIM complex formation
reactant: 222431
product: 222443
fast: false
kinetic law: 222455
has part: GO:0043241
type: Reaction
has part: GO:0006461
reactant: 222419

222203
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

222119
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

metaid_0000043
reactant: 222554
type: Reaction
is version of: http://identifiers.org/ec-code/2.7.11.1
fast: false
is version of: GO:0006468
product: 222567
kinetic law: 222580
name: PER phosphorylation
reversible: false
is version of: R00162

222554
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

metaid_0000017
constant: false
has only substance units: false
boundary condition: false
is version of: GO:0043234
in compartment: metaid_0000051
initial concentration: 1.2
has part: P49021
type: Species
name: PER_TIM complex nuclear
initial amount: NaN
has part: P07663

metaid_0000023
unit: 221999
unit: 221987
unit: 221975
name: nanoMperHour
type: SBMLUnitsDef

222275
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

294206
units: metaid_0000022
value: 2.0
name: T1_kinase_KM
type: LocalParameter

222047
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

222515
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

294175
units: metaid_0000028
value: 0.9
name: TIM_translation_rate
type: LocalParameter

294213
units: metaid_0000022
value: 0.2
name: T2_light_deact_KM
type: LocalParameter

222787
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000063
unit: 222071
unit: 222059
name: nanomolperhour
type: SBMLUnitsDef

294185
units: metaid_0000028
value: 1.2
name: C_import_rate
type: LocalParameter

metaid_0000037
kinetic law: 222407
reactant: 222395
is version of: GO:0030163
fast: false
reversible: false
name: TIM-pp decay
type: Reaction

222891
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

294165
units: metaid_0000063
value: 1.0
name: tim_max_transkr_rate
type: LocalParameter

222592
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

metaid_0000044
type: Reaction
is version of: http://identifiers.org/ec-code/2.7.11.1
reversible: false
is version of: GO:0006468
name: PER-p phosphorylation
fast: false
kinetic law: 222618
is version of: R00162
reactant: 222592
product: 222605

metaid_0000057
has version: P07663
constant: false
boundary condition: true
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: metaid_0000052
name: total PER
type: Species

221925
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000024
kinetic law: 222143
modifier: 222131
product: 222119
is: GO:0009299
fast: false
reversible: false
name: tim transkription
type: Reaction

222722
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

222826
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

294207
units: metaid_0000022
value: 2.0
name: T1_phosphatase_KM
type: LocalParameter

metaid_0000018
kinetic law: 222107
modifier: 222095
product: 222083
is version of: GO:0009299
fast: false
reversible: false
name: per transkription
type: Reaction

BIOMD0000000171
is: MODEL0243843132
units def: metaid_0000023
species: metaid_0000013
species: metaid_0000014
compartment: metaid_0000052
reaction: metaid_0000034
compartment: metaid_0000051
reaction: metaid_0000033
reaction: metaid_0000036
parameter: metaid_0000056
modified:
  W3 CDTF: Thu Jul 05 17:30:36 BST 2012
rule: metaid_0000058
is described by: http://identifiers.org/pubmed/9486845
units def: metaid_0000020
reaction: metaid_0000053
species: metaid_0000055
species: metaid_0000017
created:
  W3 CDTF: Thu May 08 11:48:48 BST 2008
is derived from: BIOMD0000000016
reaction: metaid_0000018
reaction: metaid_0000026
reaction: metaid_0000030
length unit: length
time units: metaid_0000021
notes: Leloup and Goldbeter, 1998 This model was created after the article by Leloup and Goldbeter, J Biol Rhythms 1998, Vol:13(1),pp70-87, pubmedID: 9486845 A Model for Circadian Rhythms in Drosophila Incorporating the Formation of a Complex between the PER and TIM Proteins The parameters and initial concentrations are taken to reproduce figs. 4 D,E,F in the publication. For a simulation without light dependent degradation of TIM_pp, change the the parameter v_dT_fac to 1. The light/dark phases length can be set using the parameter l_d . 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.
reaction: metaid_0000032
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
species: metaid_0000012
reaction: metaid_0000038
parameter: metaid_0000060
reaction: metaid_0000037
units def: metaid_0000039
parameter: metaid_0000019
parameter: metaid_0000066
species: metaid_0000006
species: metaid_0000008
occurs in: http://identifiers.org/taxonomy/7227
reaction: metaid_0000045
units def: metaid_0000021
reaction: metaid_0000047
parameter: metaid_0000027
type: SBMLModel
curated: true
reaction: metaid_0000024
species: metaid_0000016
is version of: GO:0007623
area units: metaid_0000005
volume units: metaid_0000004
reaction: metaid_0000035
parameter: metaid_0000064
substance units: metaid_0000020
reaction: metaid_0000029
reaction: metaid_0000041
reaction: metaid_0000050
reaction: metaid_0000043
units def: metaid_0000063
reaction: metaid_0000049
units def: metaid_0000028
species: metaid_0000011
reaction: metaid_0000031
reaction: metaid_0000040
reaction: metaid_0000046
species: metaid_0000007
reaction: metaid_0000048
rule: metaid_0000059
units def: metaid_0000022
is part of: dme04710
name: Leloup1998_CircClock_LD
reaction: metaid_0000054
species: metaid_0000057
species: metaid_0000015
rule: metaid_0000061
reaction: metaid_0000042
reaction: metaid_0000044

222748
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000030
kinetic law: 222227
modifier: 222215
product: 222203
is version of: GO:0006412
fast: false
reversible: false
name: PER tranlation
type: Reaction

221987
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

222467
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

metaid_0000050
kinetic law: 222852
product: 222839
reactant: 222826
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: TIM-pp dephosphorylation
type: Reaction

metaid_0000064
constant: true
units: dimensionless
value: 2.0
name: v_dT_fold_incr_during_light
type: Parameter

294212
units: metaid_0000022
value: 2.0
name: T2_phosphatase_KM
type: LocalParameter

metaid_0000011
has only substance units: false
is version of: P49021
initial concentration: 0.79
in compartment: metaid_0000052
type: Species
name: TIM-p
is version of: C00562
initial amount: NaN
boundary condition: false
constant: false

294168
units: metaid_0000023
value: 0.7
name: M_T_mm_decay
type: LocalParameter

metaid_0000041
kinetic law: 222503
reactant: 222491
is version of: GO:0030163
fast: false
reversible: false
name: nuclear PER_TIM compl. decay
type: Reaction

metaid_0000029
kinetic law: 222191
reactant: 222179
is version of: GO:0006402
fast: false
reversible: false
name: per mRNA decay
type: Reaction

294170
units: metaid_0000022
value: 0.2
name: decay_KM_T
type: LocalParameter

metaid_0000031
kinetic law: 222263
modifier: 222251
product: 222239
is version of: GO:0006412
fast: false
reversible: false
name: TIM translation
type: Reaction

metaid_0000019
constant: true
units: dimensionless
value: 4.0
name: transkr_rep_hill_coefficient
type: Parameter

metaid_0000021
unit: 221963
name: hours
type: SBMLUnitsDef

294191
units: metaid_0000022
value: 2.0
name: P0_kinase_KM
type: LocalParameter

metaid_0000051
is: GO:0005634
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
type: Compartment

294173
units: metaid_0000022
value: 0.2
name: M_P_decay_Km
type: LocalParameter

222323
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

294201
units: metaid_0000023
value: 8.0
name: T0_phos_rate
type: LocalParameter

222155
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

222035
exponent: -1.0
scale: -9
multipler: 1.0
kind: MOLE
type: SBMLUnit

metaid_0000012
is version of: P49021
constant: false
boundary condition: false
has only substance units: false
initial concentration: 4.65
initial amount: NaN
in compartment: metaid_0000052
name: TIM-pp
type: Species

metaid_0000039
unit: 222047
unit: 222035
unit: 222023
name: pernMperHour
type: SBMLUnitsDef

metaid_0000042
kinetic law: 222541
is version of: GO:0006886
type: Reaction
reactant: 222515
fast: false
has part: GO:0006606
reversible: true
product: 222528
has part: GO:0006611
name: PER_TIM complex shuttling

294167
units: metaid_0000022
value: 1.0
name: tim_inh_konstant
type: LocalParameter

222239
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

221975
exponent: -1.0
scale: 3
multipler: 3.6
kind: SECOND
type: SBMLUnit

294209
units: metaid_0000023
value: 1.0
name: T1_dephos_rate
type: LocalParameter

294171
units: metaid_0000023
value: 0.8
name: max_M_P_decay_rate
type: LocalParameter

metaid_0000049
kinetic law: 222813
product: 222800
reactant: 222787
is version of: GO:0006470
is version of: http://identifiers.org/ec-code/3.1.3.16
fast: false
reversible: false
name: TIM-p dephosphorylation
type: Reaction

metaid_0000032
kinetic law: 222287
reactant: 222275
is version of: GO:0030163
fast: false
reversible: false
name: PER decay
type: Reaction

metaid_0000022
unit: 221951
unit: 221938
name: nanomoleperlitre
type: SBMLUnitsDef

222761
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

metaid_0000052
is: GO:0005737
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

294174
units: metaid_0000028
value: 0.9
name: PER_translation_rate
type: LocalParameter

294200
units: metaid_0000022
value: 2.0
name: P2_phosphatase_KM
type: LocalParameter

294210
units: metaid_0000023
value: 1.0
name: T2_dephos_rate
type: LocalParameter

222528
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

294188
units: metaid_0000028
value: 0.2
name: C_export_rate
type: LocalParameter