CDMT00056
stoichiometry: 1.0
species: degraded wc1 mRNA
type: SpeciesReference

CDMT00132
stoichiometry: 1.0
species: hypoWCCn
type: SpeciesReference

CDMT00146
unit: CDMT00147
name: time
type: SBMLUnitsDef

degraded wc1 mRNA
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: c1
name: degraded_wc1_mRNA
type: Species

re12
kinetic law: CDMT00031
product: CDMT00030
reactant: CDMT00029
fast: false
reversible: false
name: re30
type: Reaction

kd hyperWCCc
constant: true
units: substance
value: 0.05
name: k_33
type: Parameter

CDMT00161
persistant: true
initial value: true
type: Trigger

kmax WC1c
constant: true
units: substance
value: 0.226
name: k_06
type: Parameter

active hypoWCCn
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.05281
in compartment: c2
name: active_hypoWCCn
type: Species

CDMT00065
stoichiometry: 1.0
species: hyperFRQn
type: SpeciesReference

CDMT00046
stoichiometry: 1.0
species: wc2 gene
type: SpeciesReference

kd WC2c
constant: true
units: substance
value: 0.085
name: k_32
type: Parameter

re41
kinetic law: CDMT00087
product: CDMT00086
reactant: CDMT00085
fast: false
reversible: false
name: re34
type: Reaction

CDMT00085
stoichiometry: 1.0
species: hyperWCCn
type: SpeciesReference

re42
kinetic law: CDMT00090
product: CDMT00089
reactant: CDMT00088
fast: false
reversible: false
name: re33
type: Reaction

hyperFRQc
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.368117
in compartment: c1
name: hyperFRQc
type: Species

CDMT00026
stoichiometry: 1.0
species: hyperWCCn
type: SpeciesReference

Kmp hypoFRQn hyperWCCn
constant: true
units: substance
value: 0.475
name: K_02
type: Parameter

CDMT00036
stoichiometry: 1.0
species: degraded WC2c
type: SpeciesReference

CDMT00095
stoichiometry: 1.0
species: hyperWCCc
type: SpeciesReference

degraded frq mRNA
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: c1
name: degraded_frq_mRNA
type: Species

re32
kinetic law: CDMT00066
product: CDMT00065
reactant: CDMT00064
fast: false
reversible: false
name: re21
type: Reaction

CDMT00147
exponent: 1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

length
unit: CDMT00145
name: length
type: SBMLUnitsDef

LP2
constant: true
units: substance
value: 0.0
name: LP2
type: Parameter

CDMT00076
stoichiometry: 1.0
species: hypoWCCc
type: SpeciesReference

wc2 mRNA
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.636098
initial amount: NaN
in compartment: c1
name: wc2_mRNA
type: Species

re23
product: CDMT00052
modifier: CDMT00053
reversible: false
reactant: CDMT00051
fast: false
kinetic law: CDMT00054
name: re09
type: Reaction

k dis WCCVVD
constant: true
units: substance
value: 1.8
name: k_28
type: Parameter

CDMT00055
stoichiometry: 1.0
species: wc1 mRNA
type: SpeciesReference

CDMT00133
stoichiometry: 1.0
species: L WCC
type: SpeciesReference

total WCCn
type: Species
initial concentration: NaN
initial amount: 0.0
has part: Q01371
boundary condition: false
has only substance units: false
in compartment: default
constant: false
has part: P78714
name: total_WCCn

n CYCLE
event assignment: CDMT00192
delay: CDMT00139
trigger: CDMT00134
use values from trigger time: true
name: n_CYCLE
type: Event

total WC1
is version of: Q01371
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_WC1
type: Species

re43
kinetic law: CDMT00093
product: CDMT00092
reactant: CDMT00091
fast: false
reversible: false
name: re25
type: Reaction

CDMT00086
stoichiometry: 1.0
species: degraded hyperWCCn
type: SpeciesReference

Period
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: Period
type: Species

CDMT00035
stoichiometry: 1.0
species: WC2c
type: SpeciesReference

re33
kinetic law: CDMT00069
product: CDMT00068
reactant: CDMT00067
fast: false
reversible: false
name: re18
type: Reaction

hyperFRQn
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.07298
in compartment: c2
name: hyperFRQn
type: Species

CDMT00077
stoichiometry: 1.0
species: hypoWCCn
type: SpeciesReference

degraded hyperWCCn
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c2
name: degraded_hyperWCCn
type: Species

s58
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.985
in compartment: default
name: line2
type: Species

CDMT00144
exponent: 2.0
scale: 0
multipler: 1.0
kind: METRE
type: SBMLUnit

LP3
constant: true
units: substance
value: 0.0
name: LP3
type: Parameter

CDMT00058
stoichiometry: 1.0
species: wc2 mRNA
type: SpeciesReference

CDMT00134
persistant: true
initial value: true
type: Trigger

re24
kinetic law: CDMT00057
product: CDMT00056
reactant: CDMT00055
fast: false
reversible: false
name: re10
type: Reaction

c1
constant: true
units: volume
size: 1.0
spatial dimensions: 3.0
name: Cytoplasm
type: Compartment

CDMT00083
stoichiometry: 1.0
species: hypoFRQc
type: SpeciesReference

re44
kinetic law: CDMT00096
product: CDMT00095
reactant: CDMT00094
fast: false
reversible: false
name: re22
type: Reaction

CDMT00038
stoichiometry: 1.0
species: wc2 mRNA
type: SpeciesReference

CDMT00097
stoichiometry: 1.0
species: time
type: SpeciesReference

ki wc2 transcription
constant: true
units: substance
value: 0.03
name: k_03i
type: Parameter

CDMT00008
stoichiometry: 1.0
species: hypoWCCc
type: SpeciesReference

time
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: time
type: Species

s57
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 1.8728
in compartment: default
name: line
type: Species

c hypoFRQ to hyperFRQ
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: c_hypoFRQ_to_hyperFRQ
type: Species

ka wc2 transcription
constant: true
units: substance
value: 0.03
name: k_03a
type: Parameter

VVDn
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c2
name: VVDn
type: Species

degraded hyperWCCc
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c1
name: degraded_hyperWCCc
type: Species

re30
kinetic law: CDMT00063
product: CDMT00062
reactant: CDMT00061
fast: false
reversible: false
name: re35
type: Reaction

CDMT00145
exponent: 1.0
scale: 0
multipler: 1.0
kind: METRE
type: SBMLUnit

light off
event assignment: CDMT00188
delay: CDMT00160
trigger: CDMT00159
use values from trigger time: true
name: light_off
type: Event

re25
kinetic law: CDMT00060
product: CDMT00059
reactant: CDMT00058
fast: false
reversible: false
name: re11
type: Reaction

WC1c
is version of: Q01371
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.039
initial amount: NaN
in compartment: c1
name: WC1c
type: Species

CDMT00064
stoichiometry: 1.0
species: hypoFRQn
type: SpeciesReference

c2
constant: true
units: volume
size: 1.0
spatial dimensions: 3.0
name: Nucleus
type: Compartment

kin VVDc
constant: true
units: substance
value: 0.3
name: k_16
type: Parameter

CDMT00023
stoichiometry: 1.0
species: WC1c
type: SpeciesReference

re45
kinetic law: CDMT00099
product: CDMT00098
reactant: CDMT00097
fast: false
reversible: false
name: Time
type: Reaction

total hyper FRQ
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_hyper_FRQ
type: Species

CDMT00098
stoichiometry: 1.0
species: http://identifiers.org/biomodels.db/BIOMD0000000437#T
type: SpeciesReference

vvd mRNA
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c1
name: vvd_mRNA
type: Species

CDMT00007
stoichiometry: 1.0
species: WC2c
type: SpeciesReference

kd vvd mRNA
constant: true
units: substance
value: 6.2
name: k_12
type: Parameter

frq level A
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: frq_level_A
type: Species

kout hyperWCCn
constant: true
units: substance
value: 0.29
name: k_19
type: Parameter

degraded VVDn
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c2
name: degraded_VVDn
type: Species

CDMT00142
exponent: 1.0
scale: 0
multipler: 1.0
kind: MOLE
type: SBMLUnit

CDMT00061
stoichiometry: 1.0
species: active hypoWCCn
type: SpeciesReference

CDMT00071
stoichiometry: 1.0
species: hyperFRQc
type: SpeciesReference

re59
kinetic law: CDMT00138
product: CDMT00137
reactant: CDMT00136
fast: false
reversible: false
name: re36
type: Reaction

kd WC1c
constant: true
units: substance
value: 0.135
name: k_31
type: Parameter

CDMT00122
stoichiometry: 1.0
species: L WCCVVDn
type: SpeciesReference

CDMT00006
stoichiometry: 1.0
species: WC1c
type: SpeciesReference

re36
kinetic law: CDMT00072
product: CDMT00071
reactant: CDMT00070
fast: false
reversible: false
name: re20
type: Reaction

CDMT00022
stoichiometry: 1.0
species: wc1 mRNA
type: SpeciesReference

I hypoFRQn hyperWCCn
constant: true
units: substance
value: 12.0
name: H_02
type: Parameter

re7
kinetic law: CDMT00025
product: CDMT00023
reactant: CDMT00022
fast: false
reversible: false
name: re06
type: Reaction

CDMT00089
stoichiometry: 1.0
species: degraded hyperWCCc
type: SpeciesReference

hypoWCCc
has only substance units: false
constant: false
type: Species
in compartment: c1
initial amount: 0.4285
name: hypoWCCc
has part: Q01371
has part: P78714
initial concentration: NaN
boundary condition: false

re46
kinetic law: CDMT00103
modifier: CDMT00102
product: CDMT00101
reactant: CDMT00100
fast: false
reversible: false
name: re04
type: Reaction

CDMT00032
stoichiometry: 1.0
species: WC1c
type: SpeciesReference

L WCCVVDn
constant: false
initial concentration: NaN
boundary condition: false
initial amount: 0.0
has only substance units: false
has part: P78714
type: Species
in compartment: c2
name: L_WCCVVDn
has part: Q01371

CDMT00143
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

CDMT00062
stoichiometry: 1.0
species: degraded active hypoWCCn
type: SpeciesReference

CDMT00059
stoichiometry: 1.0
species: degraded wc2 mRNA
type: SpeciesReference

re58
kinetic law: CDMT00135
product: CDMT00133
reactant: CDMT00132
fast: false
reversible: false
name: re26
type: Reaction

kp hypoWCCc
constant: true
units: substance
value: 0.3
name: k_22
type: Parameter

s59
constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 1.67
in compartment: default
name: line3
type: Species

re37
kinetic law: CDMT00075
product: CDMT00074
reactant: CDMT00073
fast: false
reversible: false
name: re24
type: Reaction

CDMT00123
stoichiometry: 1.0
species: hypoWCCn
type: SpeciesReference

wc1 mRNA
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.5218
initial amount: NaN
in compartment: c1
name: wc1_mRNA
type: Species

re6
kinetic law: CDMT00021
product: CDMT00019
reactant: CDMT00018
fast: false
reversible: false
name: re05
type: Reaction

WCCVVD complex disassociation
kinetic law: CDMT00125
product: CDMT00124
product: CDMT00123
reactant: CDMT00122
fast: false
reversible: false
name: re28
type: Reaction

re47
kinetic law: CDMT00106
product: CDMT00105
reactant: CDMT00104
fast: false
reversible: false
name: re08
type: Reaction

kd active hypoWCCn
constant: true
units: substance
value: 1.29
name: k_35
type: Parameter

CDMT00140
persistant: true
initial value: true
type: Trigger

kact hypoWCCn
constant: true
units: substance
value: 0.15
name: k_25
type: Parameter

hyperWCCc
initial concentration: NaN
constant: false
has part: Q01371
initial amount: 0.496374
name: hyperWCCc
boundary condition: false
has part: P78714
in compartment: c1
type: Species
has only substance units: false

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

kd frq
constant: true
units: substance
value: 2.0
name: k_09
type: Parameter

BIOMD0000000437
reaction: re58
species: total hyper FRQ
species: wc1 gene
species: hypoFRQc
parameter: kd hyperWCCn
parameter: kin hypoWCCc
reaction: re24
reaction: re43
parameter: k min wc1
is derived from: http://identifiers.org/pubmed/17965132
parameter: kdfrq hypoFRQc
parameter: Kmp hypoFRQn hyperWCCn
reaction: WCCVVD complex disassociation
species: hyperFRQn
parameter: kmaxp hypoWCCn
parameter: kd hyperFRQn
parameter: kmax wc1
reaction: re48
species: hyperWCCc
event: light on
reaction: re30
reaction: re15
parameter: kd WCCVVD
parameter: kact L WCC light
species: L WCCVVDn
name: Tseng2012 - Circadian clock of N.crassa
parameter: kd L WCC
species: total hypo FRQ
species: degraded VVDc
species: VVDn
parameter: kadd vvd light mRNA
event: light off
species: degraded hyperWCCn
species: vvd mRNA
parameter: kd VVDc
rule: CDMT00149
reaction: re51
reaction: re39
species: frq level A
compartment: c2
species: hypoWCCc
species: VVDc
parameter: kd vvd mRNA
species: http://identifiers.org/biomodels.db/BIOMD0000000437#T
species: total WC1
species: wc1 mRNA
parameter: kin hypoFRQc
parameter: LP2
species: http://identifiers.org/biomodels.db/BIOMD0000000437#X
reaction: re46
parameter: ka wc2 transcription
parameter: k VVDc
event: calculate period find frq level A
parameter: Km frq
parameter: k WCCVVD
rule: CDMT00153
type: SBMLModel
reaction: re32
species: frq mRNA
parameter: kout hyperWCCn
species: degraded hyperFFCn
parameter: kmax WC1c
rule: CDMT00152
reaction: re6
time units: CDMT00146
is derived from: BIOMD0000000299
species: wc2 mRNA
parameter: kd hyperFRQc
parameter: kd wc1
event: n CYCLE
species: total hyperWCC
reaction: re37
species: total FRQc
reaction: re18
reaction: re5
species: cycle
species: c hypoFRQ to hyperFRQ
parameter: A active hypoWCCn frq
rule: CDMT00155
parameter: off

kp hypoFRQc
constant: true
units: substance
value: 0.1
name: k_20
type: Parameter

sa101 degraded
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: c2
name: degraded_L_WCCCVVDn
type: Species

kd VVDc
constant: true
units: substance
value: 0.24
name: k_37
type: Parameter

kdp hyperWCCc
constant: true
units: substance
value: 0.3
name: k_24
type: Parameter

wc1 gene
constant: true
boundary condition: true
has only substance units: true
initial concentration: 1.0
initial amount: NaN
in compartment: c2
name: wc1_gene
type: Species

kd hyperWCCn
constant: true
units: substance
value: 0.05
name: k_34
type: Parameter

CDMT00073
stoichiometry: 1.0
species: hyperWCCc
type: SpeciesReference

degraded WC2c
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: c1
name: degraded_WC2c
type: Species

CDMT00020
stoichiometry: 1.0
species: VVDn
type: SpeciesReference

re9
kinetic law: CDMT00028
product: CDMT00027
reactant: CDMT00026
fast: false
reversible: false
name: re19
type: Reaction

CDMT00110
stoichiometry: 1.0
species: VVDc
type: SpeciesReference

re48
kinetic law: CDMT00109
product: CDMT00108
reactant: CDMT00107
fast: false
reversible: false
name: re16
type: Reaction

CDMT00120
stoichiometry: 1.0
species: L WCCVVDn
type: SpeciesReference

degraded WC1c
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: c1
name: degraded_WC1c
type: Species

degraded vvd mRNA
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c1
name: degraded_vvd_mRNA
type: Species

k WCCVVD
constant: true
units: substance
value: 20.0
name: k_27
type: Parameter

kd hyperFRQc
constant: true
units: substance
value: 0.27
name: k_29
type: Parameter

CDMT00047
stoichiometry: 1.0
species: wc2 mRNA
type: SpeciesReference

degraded active hypoWCCn
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c2
name: degraded_active_hypoWCCn
type: Species

frq mRNA
is version of: CHEBI:33699
has only substance units: false
initial amount: NaN
in compartment: c1
type: Species
constant: false
boundary condition: false
encodes: P19970
initial concentration: 0.22321
name: frq_mRNA

WC2c
is version of: P78714
constant: false
boundary condition: false
has only substance units: false
initial concentration: 6.11815
initial amount: NaN
in compartment: c1
name: WC2c
type: Species

CDMT00074
stoichiometry: 1.0
species: hypoWCCc
type: SpeciesReference

CDMT00003
stoichiometry: 1.0
species: hyperWCCn
type: SpeciesReference

kd L WCC
constant: true
units: substance
value: 6.0
name: k_36
type: Parameter

n hypoFRQ to hyperFRQ
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: n_hypoFRQ_to_hyperFRQ
type: Species

kd hyperFRQn
constant: true
units: substance
value: 0.27
name: k_30
type: Parameter

CDMT00033
stoichiometry: 1.0
species: degraded WC1c
type: SpeciesReference

re49
kinetic law: CDMT00112
product: CDMT00111
reactant: CDMT00110
fast: false
reversible: false
name: re37
type: Reaction

CDMT00111
stoichiometry: 1.0
species: degraded VVDc
type: SpeciesReference

CDMT00088
stoichiometry: 1.0
species: hyperWCCc
type: SpeciesReference

k hypoFRQc
constant: false
units: substance
value: 0.19
name: k_05
type: Parameter

area
unit: CDMT00144
name: area
type: SBMLUnitsDef

CDMT00101
stoichiometry: 1.0
species: vvd mRNA
type: SpeciesReference

kd wc1
constant: true
units: substance
value: 2.4
name: k_10
type: Parameter

degraded hyperFFCn
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: c2
name: degraded_hyperFFCn
type: Species

CDMT00013
stoichiometry: 1.0
species: frq gene
type: SpeciesReference

wc2 gene
constant: true
boundary condition: true
has only substance units: true
initial concentration: 1.0
initial amount: NaN
in compartment: c2
name: wc2_gene
type: Species

kmaxp hypoWCCn
constant: true
units: substance
value: 0.6
name: k_23
type: Parameter

cycle
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: cycle
type: Species

on
constant: true
value: 96.0
name: on
type: Parameter

WCCVVD complex formation
kinetic law: CDMT00121
reactant: CDMT00119
name: re27
fast: false
reversible: false
reactant: CDMT00020
product: CDMT00120
type: Reaction

total FRQc
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_FRQc
type: Species

k hypoWCCc
constant: true
units: substance
value: 0.472
name: k_13
type: Parameter

kout hypoFRQn
constant: true
units: substance
value: 0.1
name: k_17
type: Parameter

CDMT00159
persistant: true
initial value: true
type: Trigger

kmax frq
constant: true
units: substance
value: 7.3
name: k_01
type: Parameter

kadd vvd light mRNA
constant: true
units: substance
value: 800.0
name: k_04
type: Parameter

kd wc2
constant: true
units: substance
value: 2.5
name: k_11
type: Parameter

CDMT00100
stoichiometry: 1.0
species: vvd gene
type: SpeciesReference

s61
type: Species
initial concentration: NaN
initial amount: 0.0
has part: P78714
has part: Q01371
has only substance units: false
name: hyper_hypo_WCC
in compartment: default
constant: false
boundary condition: false

hyperWCCn
boundary condition: false
initial concentration: NaN
constant: false
has part: P78714
name: hyperWCCn
initial amount: 0.1573204
has only substance units: false
has part: Q01371
type: Species
in compartment: c2

CDMT00014
stoichiometry: 1.0
species: frq mRNA
type: SpeciesReference

total VVD
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_VVD
type: Species

CDMT00114
stoichiometry: 1.0
species: degraded VVDn
type: SpeciesReference

hypoFRQn
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.394774
in compartment: c2
name: hypoFRQn
type: Species

total WC2
is version of: P78714
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_WC2
type: Species

vvd gene
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 1.0
in compartment: c2
name: vvd_gene
type: Species

re3
reactant: CDMT00007
fast: false
reactant: CDMT00006
reversible: false
product: CDMT00008
type: Reaction
name: re13
kinetic law: CDMT00009

CDMT00128
stoichiometry: 1.0
species: sa101 degraded
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000437#X
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: X
type: Species

degraded wc2 mRNA
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: c1
name: degraded_wc2_mRNA
type: Species

CDMT00030
stoichiometry: 1.0
species: degraded hyperFFCn
type: SpeciesReference

CDMT00011
stoichiometry: 1.0
species: hypoFRQn
type: SpeciesReference

T light on
constant: true
units: substance
value: 1.0E7
name: T_light_on
type: Parameter

CDMT00019
stoichiometry: 1.0
species: hypoFRQc
type: SpeciesReference

k WC2c
constant: true
units: substance
value: 1.0
name: k_07
type: Parameter

kdfrq hypoFRQc
constant: true
units: substance
value: 0.356
name: k_09a
type: Parameter

degraded VVDc
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c1
name: degraded_VVDc
type: Species

calculate period find X
event assignment: CDMT00169
delay: CDMT00167
trigger: CDMT00166
use values from trigger time: true
name: calculate_period_find_X
type: Event

CDMT00113
stoichiometry: 1.0
species: VVDn
type: SpeciesReference

re38
kinetic law: CDMT00078
product: CDMT00077
reactant: CDMT00076
fast: false
reversible: false
name: re15
type: Reaction

re4
kinetic law: CDMT00012
product: CDMT00011
reactant: CDMT00010
fast: false
reversible: false
name: re14
type: Reaction

Km frq
constant: true
units: substance
value: 0.1
name: K_01
type: Parameter

CDMT00070
stoichiometry: 1.0
species: hypoFRQc
type: SpeciesReference

k VVDc
constant: true
units: substance
value: 0.68
name: k_08
type: Parameter

kd WCCVVD
constant: true
units: substance
value: 0.75
name: k_39
type: Parameter

default
constant: true
units: volume
size: 1.0
spatial dimensions: 3.0
type: Compartment

http://identifiers.org/biomodels.db/BIOMD0000000437#Y
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: Y
type: Species

CDMT00039
stoichiometry: 1.0
species: WC2c
type: SpeciesReference

kin hypoWCCc
constant: true
units: substance
value: 0.3
name: k_15
type: Parameter

re18
product: CDMT00042
kinetic law: CDMT00045
reversible: false
type: Reaction
fast: false
reactant: CDMT00041
modifier: CDMT00043
name: re02
modifier: CDMT00044

re39
kinetic law: CDMT00081
product: CDMT00080
reactant: CDMT00079
fast: false
reversible: false
name: re29
type: Reaction

CDMT00002
stoichiometry: 1.0
species: hypoWCCn
type: SpeciesReference

re5
reversible: false
modifier: CDMT00016
type: Reaction
name: re01
kinetic law: CDMT00017
reactant: CDMT00013
product: CDMT00014
fast: false
modifier: CDMT00015

total FRQ
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_FRQ
type: Species

L WCC
type: Species
boundary condition: false
in compartment: c2
has only substance units: false
initial amount: 0.0
name: L_WCC
initial concentration: NaN
has part: Q01371
constant: false
has part: P78714

frq gene
constant: true
boundary condition: true
has only substance units: true
initial concentration: 1.0
initial amount: NaN
in compartment: c2
name: frq_gene
type: Species

hypoWCCn
in compartment: c2
constant: false
has part: Q01371
type: Species
name: hypoWCCn
has part: P78714
boundary condition: false
initial amount: 0.47086
has only substance units: false
initial concentration: NaN

kd VVDn
constant: true
units: substance
value: 0.24
name: k_38
type: Parameter

re19
reversible: false
product: CDMT00047
fast: false
name: re03
reactant: CDMT00046
modifier: CDMT00049
type: Reaction
kinetic law: CDMT00050
modifier: CDMT00048

degraded hyperFRQc
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c1
name: degraded_hyperFRQc
type: Species

CDMT00027
stoichiometry: 1.0
species: hyperWCCc
type: SpeciesReference

kact L WCC
constant: false
units: substance
value: 0.0
name: k_26
type: Parameter

CDMT00092
stoichiometry: 1.0
species: active hypoWCCn
type: SpeciesReference

hypoFRQc
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.619449
in compartment: c1
name: hypoFRQc
type: Species

substance
unit: CDMT00142
name: substance
type: SBMLUnitsDef

k min wc1
constant: true
units: substance
value: 1.19
name: k_02
type: Parameter

CDMT00082
stoichiometry: 1.0
species: hypoFRQn
type: SpeciesReference

kp hypoFRQn
constant: true
units: substance
value: 0.1
name: k_21
type: Parameter

light on
event assignment: CDMT00189
delay: CDMT00141
trigger: CDMT00140
use values from trigger time: true
name: light_on
type: Event

CDMT00105
stoichiometry: 1.0
species: VVDc
type: SpeciesReference

kout hyperFRQn
constant: true
units: substance
value: 0.3
name: k_18
type: Parameter

total hyperWCC
initial concentration: NaN
constant: false
name: total_hyperWCC
initial amount: 0.0
boundary condition: false
has only substance units: false
has part: P78714
type: Species
in compartment: default
has part: Q01371

CDMT00079
stoichiometry: 1.0
species: hyperFRQc
type: SpeciesReference

volume
unit: CDMT00143
name: volume
type: SBMLUnitsDef

CDMT00052
stoichiometry: 1.0
species: degraded frq mRNA
type: SpeciesReference

CDMT00042
stoichiometry: 1.0
species: wc1 mRNA
type: SpeciesReference

calculate period find frq level A
event assignment: CDMT00163
delay: CDMT00162
trigger: CDMT00161
use values from trigger time: true
name: calculate_period_find_frq_level_A
type: Event

calculate period find Y
event assignment: CDMT00168
delay: CDMT00165
trigger: CDMT00164
use values from trigger time: true
name: calculate_period_find_Y
type: Event

re50
kinetic law: CDMT00115
product: CDMT00114
reactant: CDMT00113
fast: false
reversible: false
name: re38
type: Reaction

kmax light frq
constant: true
units: substance
value: 320.0
name: k_01a
type: Parameter

total hypo FRQ
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_hypo_FRQ
type: Species

CDMT00010
stoichiometry: 1.0
species: hypoFRQc
type: SpeciesReference

CDMT00018
stoichiometry: 1.0
species: frq mRNA
type: SpeciesReference

LP
constant: true
units: substance
value: 60.0
name: LP
type: Parameter

CDMT00104
stoichiometry: 1.0
species: vvd mRNA
type: SpeciesReference

CDMT00124
stoichiometry: 1.0
species: VVDn
type: SpeciesReference

off
constant: true
value: 120.0
name: off
type: Parameter

http://identifiers.org/biomodels.db/BIOMD0000000437#T
is: PATO:0000146
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: T
type: Species

CDMT00051
stoichiometry: 1.0
species: frq mRNA
type: SpeciesReference

total hypoWCC
in compartment: default
type: Species
initial concentration: NaN
constant: false
has only substance units: false
initial amount: 0.0
has part: P78714
name: total_hypoWCC
boundary condition: false
has part: Q01371

CDMT00164
persistant: true
initial value: true
type: Trigger

re17
kinetic law: CDMT00040
product: CDMT00039
reactant: CDMT00038
fast: false
reversible: false
name: re07
type: Reaction

CDMT00041
stoichiometry: 1.0
species: wc1 gene
type: SpeciesReference

CDMT00091
stoichiometry: 1.0
species: hypoWCCn
type: SpeciesReference

CDMT00119
stoichiometry: 1.0
species: L WCC
type: SpeciesReference

re51
kinetic law: CDMT00118
product: CDMT00117
reactant: CDMT00116
fast: false
reversible: false
name: re12
type: Reaction

CDMT00094
stoichiometry: 1.0
species: hypoWCCc
type: SpeciesReference

CDMT00029
stoichiometry: 1.0
species: hyperFRQn
type: SpeciesReference

CDMT00117
stoichiometry: 1.0
species: degraded vvd mRNA
type: SpeciesReference

CDMT00107
stoichiometry: 1.0
species: VVDc
type: SpeciesReference

kmax L wc1
constant: true
units: substance
value: 90.0
name: k_02a02
type: Parameter

VVDc
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: c1
name: VVDc
type: Species

total FRQn
is version of: P19970
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: default
name: total_FRQn
type: Species

CDMT00127
stoichiometry: 1.0
species: L WCCVVDn
type: SpeciesReference

kin hypoFRQc
constant: true
units: substance
value: 0.1
name: k_14
type: Parameter

CDMT00080
stoichiometry: 1.0
species: degraded hyperFRQc
type: SpeciesReference

CDMT00108
stoichiometry: 1.0
species: VVDn
type: SpeciesReference

re40
kinetic law: CDMT00084
product: CDMT00083
reactant: CDMT00082
fast: false
reversible: false
name: re17
type: Reaction

CDMT00067
stoichiometry: 1.0
species: hyperFRQn
type: SpeciesReference

A active hypoWCCn frq
constant: true
units: substance
value: 4.0
name: H_01
type: Parameter

kmax wc1
constant: true
units: substance
value: 1.2
name: k_02a01
type: Parameter

CDMT00137
stoichiometry: 1.0
species: sa101 degraded
type: SpeciesReference

re14
kinetic law: CDMT00034
product: CDMT00033
reactant: CDMT00032
fast: false
reversible: false
name: re31
type: Reaction

CDMT00116
stoichiometry: 1.0
species: vvd mRNA
type: SpeciesReference

kact L WCC light
constant: true
units: substance
value: 5.0
name: kact_L_WCC_light
type: Parameter

CDMT00126
kinetic law: CDMT00129
product: CDMT00128
reactant: CDMT00127
fast: false
reversible: false
name: re39
type: Reaction

CDMT00136
stoichiometry: 1.0
species: L WCC
type: SpeciesReference

CDMT00068
stoichiometry: 1.0
species: hyperFRQc
type: SpeciesReference

re1
kinetic law: CDMT00005
product: CDMT00003
name: re23
fast: false
reactant: CDMT00002
reversible: false
type: Reaction
modifier: CDMT00004

re15
kinetic law: CDMT00037
product: CDMT00036
reactant: CDMT00035
fast: false
reversible: false
name: re32
type: Reaction

CDMT00166
persistant: true
initial value: true
type: Trigger

kmax wc2
constant: true
units: substance
value: 1.6
name: k_03
type: Parameter

n:
  given: Yu-yao
  family: Tseng

W3 CDTF: Tue Feb 26 14:39:12 GMT 2013

W3 CDTF: Thu Jun 06 12:54:51 BST 2013