BIOMD0000000437
type: SBMLModel
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
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
species: total FRQc
reaction: re37
reaction: re18
reaction: re5
species: cycle
species: c hypoFRQ to hyperFRQ
parameter: A active hypoWCCn frq
rule: CDMT00155
parameter: off

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

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

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

volume
type: SBMLUnitsDef
unit: CDMT00143
name: volume

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

CDMT00133
type: SpeciesReference
stoichiometry: 1.0
species: L WCC

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

CDMT00132
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCn

total hyper FRQ
type: Species
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

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

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

hypoFRQc
type: Species
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

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

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

substance
type: SBMLUnitsDef
unit: CDMT00142
name: substance

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

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

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

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

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

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

CDMT00055
type: SpeciesReference
stoichiometry: 1.0
species: wc1 mRNA

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

CDMT00092
type: SpeciesReference
stoichiometry: 1.0
species: active hypoWCCn

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

CDMT00091
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCn

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

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

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

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

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

CDMT00124
type: SpeciesReference
stoichiometry: 1.0
species: VVDn

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

CDMT00123
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCn

CDMT00122
type: SpeciesReference
stoichiometry: 1.0
species: L WCCVVDn

hyperFRQn
type: Species
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

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

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

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

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

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

CDMT00108
type: SpeciesReference
stoichiometry: 1.0
species: VVDn

CDMT00107
type: SpeciesReference
stoichiometry: 1.0
species: VVDc

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

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

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

CDMT00140
type: Trigger
persistant: true
initial value: true

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

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

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

CDMT00061
type: SpeciesReference
stoichiometry: 1.0
species: active hypoWCCn

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

WC2c
type: Species
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

CDMT00036
type: SpeciesReference
stoichiometry: 1.0
species: degraded WC2c

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

CDMT00035
type: SpeciesReference
stoichiometry: 1.0
species: WC2c

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

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

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

total hypo FRQ
type: Species
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

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

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

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

CDMT00159
type: Trigger
persistant: true
initial value: true

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

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

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

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

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

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

CDMT00116
type: SpeciesReference
stoichiometry: 1.0
species: vvd mRNA

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

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

CDMT00080
type: SpeciesReference
stoichiometry: 1.0
species: degraded hyperFRQc

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

CDMT00079
type: SpeciesReference
stoichiometry: 1.0
species: hyperFRQc

frq level A
type: Species
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

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

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

http://identifiers.org/biomodels.db/BIOMD0000000437#T
type: Species
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

total WC1
type: Species
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

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

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

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

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

CDMT00101
type: SpeciesReference
stoichiometry: 1.0
species: vvd mRNA

CDMT00100
type: SpeciesReference
stoichiometry: 1.0
species: vvd gene

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

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

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

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

CDMT00161
type: Trigger
persistant: true
initial value: true

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

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

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

hypoFRQn
type: Species
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

CDMT00065
type: SpeciesReference
stoichiometry: 1.0
species: hyperFRQn

CDMT00064
type: SpeciesReference
stoichiometry: 1.0
species: hypoFRQn

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

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

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

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

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

CDMT00019
type: SpeciesReference
stoichiometry: 1.0
species: hypoFRQc

CDMT00018
type: SpeciesReference
stoichiometry: 1.0
species: frq mRNA

CDMT00146
type: SBMLUnitsDef
unit: CDMT00147
name: time

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

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

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

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

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

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

CDMT00134
type: Trigger
persistant: true
initial value: true

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

total FRQc
type: Species
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

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

CDMT00074
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCc

CDMT00073
type: SpeciesReference
stoichiometry: 1.0
species: hyperWCCc

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

CDMT00042
type: SpeciesReference
stoichiometry: 1.0
species: wc1 mRNA

CDMT00041
type: SpeciesReference
stoichiometry: 1.0
species: wc1 gene

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

CDMT00013
type: SpeciesReference
stoichiometry: 1.0
species: frq gene

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

CDMT00014
type: SpeciesReference
stoichiometry: 1.0
species: frq mRNA

c hypoFRQ to hyperFRQ
type: Species
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

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

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

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

hyperWCCn
type: Species
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
in compartment: c2

total FRQn
type: Species
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

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

CDMT00137
type: SpeciesReference
stoichiometry: 1.0
species: sa101 degraded

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

CDMT00136
type: SpeciesReference
stoichiometry: 1.0
species: L WCC

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

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

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

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

CDMT00058
type: SpeciesReference
stoichiometry: 1.0
species: wc2 mRNA

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

CDMT00095
type: SpeciesReference
stoichiometry: 1.0
species: hyperWCCc

CDMT00094
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCc

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

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

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

CDMT00164
type: Trigger
persistant: true
initial value: true

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

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

WC1c
type: Species
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

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

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

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

CDMT00111
type: SpeciesReference
stoichiometry: 1.0
species: degraded VVDc

CDMT00110
type: SpeciesReference
stoichiometry: 1.0
species: VVDc

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

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

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

CDMT00007
type: SpeciesReference
stoichiometry: 1.0
species: WC2c

CDMT00006
type: SpeciesReference
stoichiometry: 1.0
species: WC1c

CDMT00008
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCc

area
type: SBMLUnitsDef
unit: CDMT00144
name: area

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

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

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

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

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

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

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

CDMT00027
type: SpeciesReference
stoichiometry: 1.0
species: hyperWCCc

CDMT00026
type: SpeciesReference
stoichiometry: 1.0
species: hyperWCCn

total hypoWCC
type: Species
in compartment: default
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

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

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

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

CDMT00051
type: SpeciesReference
stoichiometry: 1.0
species: frq mRNA

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

CDMT00089
type: SpeciesReference
stoichiometry: 1.0
species: degraded hyperWCCc

CDMT00088
type: SpeciesReference
stoichiometry: 1.0
species: hyperWCCc

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

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

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

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

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

length
type: SBMLUnitsDef
unit: CDMT00145
name: length

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

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

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

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

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

n hypoFRQ to hyperFRQ
type: Species
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

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

CDMT00105
type: SpeciesReference
stoichiometry: 1.0
species: VVDc

CDMT00104
type: SpeciesReference
stoichiometry: 1.0
species: vvd mRNA

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

CDMT00033
type: SpeciesReference
stoichiometry: 1.0
species: degraded WC1c

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

CDMT00032
type: SpeciesReference
stoichiometry: 1.0
species: WC1c

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

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

CDMT00003
type: SpeciesReference
stoichiometry: 1.0
species: hyperWCCn

CDMT00002
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCn

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

CDMT00068
type: SpeciesReference
stoichiometry: 1.0
species: hyperFRQc

CDMT00067
type: SpeciesReference
stoichiometry: 1.0
species: hyperFRQn

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

CDMT00023
type: SpeciesReference
stoichiometry: 1.0
species: WC1c

CDMT00022
type: SpeciesReference
stoichiometry: 1.0
species: wc1 mRNA

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

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

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

CDMT00128
type: SpeciesReference
stoichiometry: 1.0
species: sa101 degraded

CDMT00127
type: SpeciesReference
stoichiometry: 1.0
species: L WCCVVDn

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

CDMT00114
type: SpeciesReference
stoichiometry: 1.0
species: degraded VVDn

CDMT00113
type: SpeciesReference
stoichiometry: 1.0
species: VVDn

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

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

CDMT00047
type: SpeciesReference
stoichiometry: 1.0
species: wc2 mRNA

CDMT00046
type: SpeciesReference
stoichiometry: 1.0
species: wc2 gene

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

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

CDMT00077
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCn

CDMT00076
type: SpeciesReference
stoichiometry: 1.0
species: hypoWCCc

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

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

total FRQ
type: Species
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

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

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

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

CDMT00086
type: SpeciesReference
stoichiometry: 1.0
species: degraded hyperWCCn

CDMT00085
type: SpeciesReference
stoichiometry: 1.0
species: hyperWCCn

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

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

CDMT00097
type: SpeciesReference
stoichiometry: 1.0
species: time

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

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

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

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

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

CDMT00030
type: SpeciesReference
stoichiometry: 1.0
species: degraded hyperFFCn

CDMT00029
type: SpeciesReference
stoichiometry: 1.0
species: hyperFRQn

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

CDMT00083
type: SpeciesReference
stoichiometry: 1.0
species: hypoFRQc

CDMT00082
type: SpeciesReference
stoichiometry: 1.0
species: hypoFRQn

total WC2
type: Species
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

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

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

CDMT00119
type: SpeciesReference
stoichiometry: 1.0
species: L WCC

CDMT00020
type: SpeciesReference
stoichiometry: 1.0
species: VVDn

CDMT00120
type: SpeciesReference
stoichiometry: 1.0
species: L WCCVVDn

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

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

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

CDMT00071
type: SpeciesReference
stoichiometry: 1.0
species: hyperFRQc

CDMT00070
type: SpeciesReference
stoichiometry: 1.0
species: hypoFRQc

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

CDMT00039
type: SpeciesReference
stoichiometry: 1.0
species: WC2c

CDMT00038
type: SpeciesReference
stoichiometry: 1.0
species: wc2 mRNA

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

CDMT00011
type: SpeciesReference
stoichiometry: 1.0
species: hypoFRQn

CDMT00010
type: SpeciesReference
stoichiometry: 1.0
species: hypoFRQc

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

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

n:
  given: Yu-yao
  family: Tseng

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

CDMT00166
type: Trigger
persistant: true
initial value: true

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

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