BIOMD0000000171
type: SBMLModel
created:
  W3 CDTF: Thu May 08 11:48:48 BST 2008
is: MODEL0243843132
units def: metaid_0000023
species: metaid_0000013
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
species: metaid_0000014
compartment: metaid_0000052
reaction: metaid_0000034
compartment: metaid_0000051
reaction: metaid_0000033
reaction: metaid_0000036
parameter: metaid_0000056
rule: metaid_0000058
is described by: http://identifiers.org/pubmed/9486845
units def: metaid_0000020
reaction: metaid_0000053
species: metaid_0000055
species: metaid_0000017
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
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
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
modified:
  W3 CDTF: Thu Jul 05 17:30:36 BST 2012
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
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reaction: metaid_0000042
reaction: metaid_0000044

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

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

221987
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exponent: 1.0
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kind: MOLE

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

metaid_0000013
type: Species
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

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

metaid_0000014
type: Species
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constant: false
has only substance units: false
boundary condition: false
is version of: C00562
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initial amount: NaN
name: PER-p

metaid_0000034
type: Reaction
kinetic law: 222335
reactant: 222323
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fast: false
reversible: false
name: PER-pp decay

222323
type: SpeciesReference
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species: metaid_0000015

metaid_0000015
type: Species
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name: PER-pp
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metaid_0000051
type: Compartment
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constant: true
units: litre
size: 1.0
spatial dimensions: 3.0

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

222299
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

222371
type: SpeciesReference
stoichiometry: 1.0
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metaid_0000011
type: Species
has only substance units: false
is version of: P49021
initial concentration: 0.79
in compartment: metaid_0000052
name: TIM-p
is version of: C00562
initial amount: NaN
boundary condition: false
constant: false

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

metaid_0000021
type: SBMLUnitsDef
unit: 221963
name: hours

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

metaid_0000020
type: SBMLUnitsDef
unit: 221925
name: nanomolar

221925
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exponent: 1.0
scale: -9
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kind: MOLE

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

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

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

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

221938
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kind: MOLE

222865
type: SpeciesReference
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species: metaid_0000012

metaid_0000012
type: Species
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

metaid_0000055
type: Species
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

metaid_0000017
type: Species
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
name: PER_TIM complex nuclear
initial amount: NaN
has part: P07663

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

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

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

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

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

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

222083
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

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

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

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

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

222155
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

metaid_0000006
type: Species
constant: false
is version of: CHEBI:33699
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_0000030
type: Reaction
kinetic law: 222227
modifier: 222215
product: 222203
is version of: GO:0006412
fast: false
reversible: false
name: PER tranlation

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

metaid_0000028
type: SBMLUnitsDef
unit: 222011
name: perhour

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

222203
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

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

222275
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

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

222431
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

222443
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000016
type: Species
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
in compartment: metaid_0000052
initial amount: NaN
has part: P07663
constant: false

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

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

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

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

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

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

222419
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

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

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

222395
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

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

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

metaid_0000008
type: Species
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

metaid_0000045
type: Reaction
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

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

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

222644
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

222631
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

222709
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

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

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

222722
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

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

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

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

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

222119
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

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

222347
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

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

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

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

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

222179
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

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

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

222491
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

metaid_0000050
type: Reaction
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

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

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

222839
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

222826
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000043
type: Reaction
reactant: 222554
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
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

222567
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

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

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

metaid_0000049
type: Reaction
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

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

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

222800
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

222787
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

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

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

222239
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

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

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

222467
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000046
type: Reaction
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

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

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

222683
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

222670
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species: metaid_0000015

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

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

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

222748
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

222761
type: SpeciesReference
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species: metaid_0000012

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

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

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

222891
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

metaid_0000057
type: Species
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

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

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

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

222515
type: SpeciesReference
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species: metaid_0000016

222528
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

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

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

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

222592
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

222605
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015