BIOMD0000000160
type: SBMLModel
species: metaid_0000072
species: metaid_0000070
area units: metaid_0000005
parameter: metaid_0000006
parameter: metaid_0000009
parameter: metaid_0000003
parameter: metaid_0000008
parameter: metaid_0000017
species: metaid_0000076
parameter: metaid_0000036
parameter: metaid_0000020
reaction: metaid_0000116
reaction: metaid_0000109
reaction: metaid_0000118
reaction: metaid_0000086
reaction: metaid_0000095
reaction: metaid_0000089
parameter: metaid_0000035
reaction: metaid_0000088
reaction: metaid_0000082
reaction: metaid_0000091
species: metaid_0000060
species: metaid_0000064
species: metaid_0000066
species: metaid_0000056
reaction: metaid_0000096
parameter: metaid_0000011
parameter: metaid_0000043
reaction: metaid_0000092
occurs in: http://identifiers.org/taxonomy/7227
parameter: metaid_0000019
parameter: metaid_0000038
parameter: metaid_0000047
reaction: metaid_0000102
parameter: metaid_0000031
parameter: metaid_0000012
parameter: metaid_0000033
reaction: metaid_0000099
reaction: metaid_0000111
species: metaid_0000058
is: GO:0045187
parameter: metaid_0000014
parameter: metaid_0000028
parameter: metaid_0000037
species: metaid_0000069
is part of: dme04711
parameter: metaid_0000041
parameter: metaid_0000040
parameter: metaid_0000046
reaction: metaid_0000110
reaction: metaid_0000101
species: metaid_0000061
species: metaid_0000063
species: metaid_0000053
parameter: metaid_0000005
species: metaid_0000065
parameter: metaid_0000004
species: metaid_0000055
reaction: metaid_0000104
reaction: metaid_0000103
reaction: metaid_0000106
reaction: metaid_0000083
parameter: metaid_0000023
reaction: metaid_0000097
parameter: metaid_0000022
units def: metaid_0000119
reaction: metaid_0000093
parameter: metaid_0000039
reaction: metaid_0000113
species: metaid_0000068
parameter: metaid_0000042
parameter: metaid_0000013
parameter: metaid_0000045
name: Xie2007_CircClock
parameter: metaid_0000044
reaction: metaid_0000112
volume units: metaid_0000084
parameter: metaid_0000007
parameter: metaid_0000015

metaid_0000072
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0431
in compartment: metaid_0000051
name: CCbindingPer

metaid_0000051
type: Compartment
is: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: wholeCell

metaid_0000070
type: Species
is version of: Q59E16
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.7527
initial amount: NaN
in compartment: metaid_0000051
name: TIM

metaid_0000006
type: Parameter
constant: true
value: 51.0

metaid_0000009
type: Parameter
constant: true
value: 11.0

metaid_0000003
type: Parameter
constant: true
value: 15.06

metaid_0000008
type: Parameter
constant: true
value: 36.0

metaid_0000017
type: Parameter
constant: true
value: 2.93

metaid_0000076
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.426
in compartment: metaid_0000051
name: PDPbindingclkp

metaid_0000036
type: Parameter
constant: true
value: 0.053

metaid_0000020
type: Parameter
constant: true
value: 9.831

metaid_0000116
type: Reaction
kinetic law: 455733
reactant: 455721
is version of: GO:0043433
fast: false
reversible: false
name: PDP unbinding clk promoter

455721
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000076

metaid_0000109
type: Reaction
kinetic law: 455493
reactant: 455481
is version of: GO:0006357
fast: false
reversible: false
name: CC Unbinding probability in vri promoter

455481
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000073

metaid_0000073
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0585
in compartment: metaid_0000051
name: CCbindingvri

metaid_0000118
type: Reaction
kinetic law: 455793
reactant: 455781
is version of: GO:0006357
fast: false
reversible: false
name: CC Unbinding probability in tim promoter

455781
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000077

metaid_0000077
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.043
in compartment: metaid_0000051
name: CCbindingtim

metaid_0000086
type: Reaction
kinetic law: 454663
modifier: 454651
modifier: 454638
product: 454626
is version of: GO:0006351
fast: false
reversible: false
name: per transcription

metaid_0000056
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.003185
initial amount: NaN
in compartment: metaid_0000051
name: perp

454626
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000058

metaid_0000058
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.2395
initial amount: NaN
in compartment: metaid_0000051
name: perm

metaid_0000095
type: Reaction
reversible: false
product: 454939
is version of: GO:0006351
kinetic law: 454988
fast: false
modifier: 454963
modifier: 454975
modifier: 454951
name: clk transcription

454939
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000057

metaid_0000057
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.2583
initial amount: NaN
in compartment: metaid_0000051
name: clkm

metaid_0000055
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.003185
initial amount: NaN
in compartment: metaid_0000051
name: clkp

metaid_0000075
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.489
in compartment: metaid_0000051
name: VRIbindingclkp

metaid_0000089
type: Reaction
kinetic law: 454771
modifier: 454759
product: 454747
is version of: GO:0006412
fast: false
reversible: false
name: vrim translation

metaid_0000061
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.2571
initial amount: NaN
in compartment: metaid_0000051
name: vrim

454747
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

metaid_0000062
type: Species
is: Q9VMS4
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.175
initial amount: NaN
in compartment: metaid_0000051
name: VRI

metaid_0000035
type: Parameter
constant: true
value: 0.952

metaid_0000088
type: Reaction
kinetic law: 454735
reactant: 454723
is version of: GO:0006402
fast: false
reversible: false
name: Degradation of vri mRNA

454723
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000061

metaid_0000082
type: Reaction
kinetic law: 454518
reactant: 454506
is version of: GO:0006402
fast: false
reversible: false
name: Degradation of clk mRNA

454506
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000057

metaid_0000091
type: Reaction
kinetic law: 454843
modifier: 454831
modifier: 454819
product: 454807
is version of: GO:0006351
fast: false
reversible: false
name: pdp transcription

metaid_0000063
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.003185
initial amount: NaN
in compartment: metaid_0000051
name: pdpp

metaid_0000074
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.08
in compartment: metaid_0000051
name: CCbindingpdp

454807
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000064

metaid_0000064
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.3175
initial amount: NaN
in compartment: metaid_0000051
name: pdpm

metaid_0000060
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.003185
initial amount: NaN
in compartment: metaid_0000051
name: vrip

metaid_0000066
type: Species
is version of: O61735
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.6628
initial amount: NaN
in compartment: metaid_0000051
name: CLK

metaid_0000096
type: Reaction
kinetic law: 455036
product: 455024
reactant: 455012
reactant: 455000
is version of: GO:0046982
fast: false
reversible: false
name: CLK CYC association

455024
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000053

metaid_0000053
type: Species
constant: false
initial concentration: 0.5566
initial amount: NaN
boundary condition: false
name: CC
has part: O61734
in compartment: metaid_0000051
has only substance units: false
has part: O61735

455012
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000071

metaid_0000071
type: Species
is version of: O61734
constant: true
boundary condition: true
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: metaid_0000051
name: CYC

455000
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

metaid_0000011
type: Parameter
constant: true
value: 1.226

metaid_0000043
type: Parameter
constant: true
value: 36.0

metaid_0000092
type: Reaction
kinetic law: 454867
reactant: 454855
is version of: GO:0006402
fast: false
reversible: false
name: Degradation of pdp mRNA

454855
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000064

metaid_0000019
type: Parameter
constant: true
value: 16.86

metaid_0000038
type: Parameter
constant: true
value: 35.0

metaid_0000047
type: Parameter
constant: true
value: 5.0

metaid_0000102
type: Reaction
kinetic law: 455277
modifier: 455265
modifier: 455253
product: 455241
is version of: GO:0006351
fast: false
reversible: false
name: tim transcription

metaid_0000068
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.003185
initial amount: NaN
in compartment: metaid_0000051
name: timp

455241
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000069

metaid_0000069
type: Species
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.2395
initial amount: NaN
in compartment: metaid_0000051
name: timm

metaid_0000031
type: Parameter
constant: true
value: 0.643

metaid_0000012
type: Parameter
constant: true
value: 1.42

metaid_0000033
type: Parameter
constant: true
value: 1.155

metaid_0000099
type: Reaction
kinetic law: 455157
product: 455145
reactant: 455133
reactant: 455121
is version of: GO:0046982
fast: false
reversible: false
name: PER TIM association

455145
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000059
type: Species
initial concentration: 0.4014
name: PT
has part: P07663
has part: Q59E16
has only substance units: false
boundary condition: false
initial amount: NaN
in compartment: metaid_0000051
constant: false

455133
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000070

455121
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000067

metaid_0000067
type: Species
is version of: P07663
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.7527
initial amount: NaN
in compartment: metaid_0000051
name: PER

metaid_0000111
type: Reaction
kinetic law: 455553
reactant: 455541
is version of: GO:0006357
fast: false
reversible: false
name: CC Unbinding probability in pdp1 promoter

455541
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000074

metaid_0000014
type: Parameter
constant: true
value: 0.2

metaid_0000028
type: Parameter
constant: true
value: 0.276

metaid_0000037
type: Parameter
constant: true
value: 0.156

metaid_0000041
type: Parameter
constant: true
value: 0.62

metaid_0000040
type: Parameter
constant: true
value: 0.279

metaid_0000046
type: Parameter
constant: true
value: 11.0

metaid_0000110
type: Reaction
kinetic law: 455529
modifier: 455517
product: 455505
is version of: GO:0006357
fast: false
reversible: false
name: CC binding probability in vri promoter

455505
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000073

metaid_0000101
type: Reaction
kinetic law: 455229
reactant: 455217
is version of: GO:0044257
fast: false
reversible: false
name: PER protein degradation

455217
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000067

metaid_0000005
type: Parameter
constant: true
value: 0.262

metaid_0000065
type: Species
is version of: Q9TW49
constant: false
boundary condition: false
has only substance units: false
initial concentration: 4.1953
initial amount: NaN
in compartment: metaid_0000051
name: PDP

metaid_0000004
type: Parameter
constant: true
value: 0.069

metaid_0000104
type: Reaction
kinetic law: 455337
modifier: 455325
product: 455313
is version of: GO:0006412
fast: false
reversible: false
name: timm translation

455313
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000070

metaid_0000103
type: Reaction
kinetic law: 455301
reactant: 455289
is version of: GO:0006402
fast: false
reversible: false
name: Degradation of tim mRNA

455289
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000069

metaid_0000106
type: Reaction
kinetic law: 455409
product: 455397
product: 455385
reactant: 455373
is version of: GO:0046982
fast: false
reversible: false
name: CC PT dimer dissociation

455397
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

455385
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000053

455373
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000054

metaid_0000054
type: Species
in compartment: metaid_0000051
initial amount: NaN
has part: Q59E16
initial concentration: 0.4982
has part: O61735
has part: P07663
constant: false
has only substance units: false
name: CCPT
has part: O61734
boundary condition: false

metaid_0000083
type: Reaction
kinetic law: 454554
modifier: 454542
product: 454530
is version of: GO:0006412
fast: false
reversible: false
name: clkm translation

454530
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

metaid_0000023
type: Parameter
constant: true
value: 7.89

metaid_0000097
type: Reaction
kinetic law: 455061
reactant: 455049
is version of: GO:0044257
fast: false
reversible: false
name: CLK protein degradation

455049
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

metaid_0000022
type: Parameter
constant: true
value: 0.06

metaid_0000119
type: SBMLUnitsDef
unit: 454362
name: nano mole

454362
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000093
type: Reaction
kinetic law: 454903
modifier: 454891
product: 454879
is version of: GO:0006412
fast: false
reversible: false
name: pdpm translation

454879
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000065

metaid_0000039
type: Parameter
constant: true
value: 0.184

metaid_0000113
type: Reaction
kinetic law: 455637
modifier: 455625
modifier: 455613
product: 455601
is version of: GO:0030528
fast: false
reversible: false
name: VRI binding clk promoter

455601
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000075

metaid_0000042
type: Parameter
constant: true
value: 0.053

metaid_0000013
type: Parameter
constant: true
value: 2.349

metaid_0000045
type: Parameter
constant: true
value: 0.262

metaid_0000044
type: Parameter
constant: true
value: 0.069

metaid_0000112
type: Reaction
kinetic law: 455589
modifier: 455577
product: 455565
is version of: GO:0006357
fast: false
reversible: false
name: CC binding probability in pdp1 promoter

455565
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000074

metaid_0000007
type: Parameter
constant: true
value: 0.053

metaid_0000015
type: Parameter
constant: true
value: 0.89

metaid_0000049
type: Parameter
constant: true
value: 6.0

metaid_0000048
type: Parameter
constant: true
value: 4.0

metaid_0000108
type: Reaction
kinetic law: 455469
reactant: 455457
is version of: GO:0006357
fast: false
reversible: false
name: CC Unbinding probability in per promoter

455457
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000072

metaid_0000107
type: Reaction
kinetic law: 455445
modifier: 455433
product: 455421
is version of: GO:0006357
fast: false
reversible: false
name: CC binding probability in per promoter

455421
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000072

metaid_0000021
type: Parameter
constant: true
value: 0.07

metaid_0000120
type: SBMLUnitsDef
unit: 454374
name: hour

454374
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 3600.0
kind: SECOND

metaid_0000078
type: Reaction
kinetic law: 454422
product: 454410
reactant: 454398
reactant: 454386
is version of: GO:0046982
fast: false
reversible: false
name: CC PT association

454410
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000054

454398
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

454386
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000053

metaid_0000087
type: Reaction
kinetic law: 454711
modifier: 454699
modifier: 454687
product: 454675
is version of: GO:0006351
fast: false
reversible: false
name: vri transcription

454675
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000061

metaid_0000016
type: Parameter
constant: true
value: 1.1

metaid_0000025
type: Parameter
constant: true
value: 1.87

metaid_0000115
type: Reaction
kinetic law: 455709
modifier: 455697
modifier: 455685
product: 455673
is version of: GO:0003700
fast: false
reversible: false
name: PDP binding clk promoter

455673
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000076

metaid_0000117
type: Reaction
kinetic law: 455769
modifier: 455757
product: 455745
is version of: GO:0006357
fast: false
reversible: false
name: CC binding probability in tim promoter

455745
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000077

metaid_0000094
type: Reaction
kinetic law: 454927
reactant: 454915
is version of: GO:0044257
fast: false
reversible: false
name: PDP protein degradation

454915
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000065

metaid_0000034
type: Parameter
constant: true
value: 1.043

metaid_0000090
type: Reaction
kinetic law: 454795
reactant: 454783
is version of: GO:0044257
fast: false
reversible: false
name: VRI protein degradation

454783
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000062

W3 CDTF: Thu Jul 05 15:37:46 BST 2012

metaid_0000105
type: Reaction
kinetic law: 455361
reactant: 455349
is version of: GO:0044257
fast: false
reversible: false
name: TIM protein degradation

455349
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000070

metaid_0000114
type: Reaction
kinetic law: 455661
reactant: 455649
is version of: GO:0030528
fast: false
reversible: false
name: VRI unbinding clk promoter

455649
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000075

metaid_0000085
type: Reaction
kinetic law: 454614
modifier: 454602
product: 454590
is version of: GO:0006412
fast: false
reversible: false
name: perm translation

454590
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000067

metaid_0000084
type: Reaction
kinetic law: 454578
reactant: 454566
is version of: GO:0006402
fast: false
reversible: false
name: Degradation of per mRNA

454566
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000058

metaid_0000010
type: Parameter
constant: true
value: 0.028

metaid_0000024
type: Parameter
constant: true
value: 14.68

metaid_0000081
type: Reaction
kinetic law: 454494
reactant: 454482
is version of: GO:0044257
fast: false
reversible: false
name: Degradation of PER TIM dimer

454482
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000080
type: Reaction
kinetic law: 454470
reactant: 454458
is version of: GO:0044257
fast: false
reversible: false
name: Degradation of CC PT dimer

454458
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000054

metaid_0000018
type: Parameter
constant: true
value: 0.62

metaid_0000027
type: Parameter
constant: true
value: 0.062

metaid_0000026
type: Parameter
constant: true
value: 0.1

metaid_0000029
type: Parameter
constant: true
value: 0.145

metaid_0000030
type: Parameter
constant: true
value: 125.54

metaid_0000032
type: Parameter
constant: true
value: 1.858

metaid_0000079
type: Reaction
kinetic law: 454446
reactant: 454434
is version of: GO:0044257
fast: false
reversible: false
name: Degradation of CLK CYK dimer

454434
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000053

metaid_0000100
type: Reaction
kinetic law: 455205
product: 455193
product: 455181
reactant: 455169
is version of: GO:0043624
fast: false
reversible: false
name: PER TIM dissociation

455193
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000070

455181
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000067

455169
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000059

metaid_0000098
type: Reaction
kinetic law: 455109
product: 455097
product: 455085
reactant: 455073
is version of: GO:0043624
fast: false
reversible: false
name: CLK CYC dissociation

455097
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000071

455085
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000066

455073
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000053

W3 CDTF: Tue Jan 22 07:26:48 GMT 2008

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri