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Below is displayed the model view of the selected project. Model view is shown in the form of the model overview page for the currently selected model. The central feature of the model view is the model scheme that shows individual model components of selected model. The navigation panel on the left allows you to browse the biological structure of the model. Manipulation with the navigation panel is realized by unfolding the items in the navigation tree and clicking on a requested system level.

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Reactions Tab
Reactions Tab contains information regarding the modeled reactions. After clicking on the particular reaction header, the reacting components and relevant kinetic parameters are displayed.

Parameters Tab
All quantitative parameters are managed under Parameters Tab. Constants are separated from assigned quantities.

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Simulation and SBML export are available by clicking on appropriate buttons at the bottom of the tab. All relevant settings of initial conditions, parameters, options and datasets are listed in respective folders.

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Conservation analysis, modes analysis and matrix analysis are available by clicking on appropriate buttons.

Experiments Tab
Experiments tab contains list of all experiments related to selected model.

Hertel et al. 2013

Hertel S, Brettschneider Ch, Ilka Axmann M (2013) Revealing a Two-Loop Transcriptional Feedback
Mechanism in the Cyanobacterial Circadian Clock. PLOS Computational Biology 9(3) e1002966.

Hertel S, Brettschneider Ch, Ilka Axmann M (2013) Revealing a Two-Loop Transcriptional Feedback
Mechanism in the Cyanobacterial Circadian Clock. PLOS Computational Biology 9(3) e1002966.


publication: Hertel et al. 2013
Contains:
Initial expression: 1
Simulation type: fixed
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 2*AT
Simulation type: reaction
Details
Initial expression: 0.998*CT
Simulation type: reaction
Details
Initial expression: 0.001*CT
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0.001*CT
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Initial expression: 0
Simulation type: reaction
Details
Equation: KaiA ->
Function: Mass Action (irreversible)
Reaction rate: k4_a*KaiA
Kinetic rate constant Value
k4_a 0.3278
Details
Equation: -> KaiA
Modifiers: kaiA_mRNA
Function: Specific translation from mRNA (Hertel et al.) (irreversible)
Reaction rate: k2_a*kaiA_mRNA
Kinetic rate constant Value
k2_a 0.3497
Details
Equation: -> kaiA_mRNA
Function: General flux (reversible)
Reaction rate: k1_a
Kinetic rate constant Value
k1_a 0.0117
Details
Equation: KaiBC_D ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_D
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiBC_D -> KaiC_D
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_D
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiBC_D -> KaiBC_S
Function: Mass Action (irreversible)
Reaction rate: ksdN*KaiBC_D
Kinetic rate constant Value
ksdN 0.34
Details
Equation: KaiBC_D -> KaiBC_T
Function: Mass Action (irreversible)
Reaction rate: ktdN*KaiBC_D
Kinetic rate constant Value
ktdN 0
Details
Equation: KaiBC_S ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_S
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiBC_S -> KaiBC_U
Function: Mass Action (irreversible)
Reaction rate: kusN*KaiBC_S
Kinetic rate constant Value
kusN 0.12
Details
Equation: KaiBC_S -> KaiC_S
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_S
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiBC_S -> KaiBC_D
Function: Mass Action (irreversible)
Reaction rate: kdsN*KaiBC_S
Kinetic rate constant Value
kdsN 0
Details
Equation: KaiBC_T ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_T
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiBC_T -> KaiBC_U
Function: Mass Action (irreversible)
Reaction rate: kutN*KaiBC_T
Kinetic rate constant Value
kutN 0.22
Details
Equation: KaiBC_T -> KaiC_T
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_T
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiBC_T -> KaiBC_D
Function: Mass Action (irreversible)
Reaction rate: kdtN*KaiBC_T
Kinetic rate constant Value
kdtN 0.13
Details
Equation: KaiBC_U ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_U
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiBC_U -> KaiC_U
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_U
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiBC_U -> KaiBC_S
Function: Mass Action (irreversible)
Reaction rate: ksuN*KaiBC_U
Kinetic rate constant Value
ksuN 0
Details
Equation: KaiBC_U -> KaiBC_T
Function: Mass Action (irreversible)
Reaction rate: ktuN*KaiBC_U
Kinetic rate constant Value
ktuN 0.01
Details
Equation: KaiBC_U -> KaiC6_U
Function: Specific protein pool exchange (Hertel et al.) (irreversible)
Reaction rate: cu * KaiBC_U * (KaiBC_U/C_B)^5
Kinetic rate constant Value
cu 0
C_B "KaiBC_U" + "KaiBC_T" + "KaiBC_S" + "KaiBC_D"
Details
Equation: -> KaiC_U
Modifiers: kaiBC_mRNA
Function: Specific translation from mRNA (Hertel et al.) (irreversible)
Reaction rate: k2_bc*kaiBC_mRNA
Kinetic rate constant Value
k2_bc 0.0457
Details
Equation: KaiC_D -> KaiC6_D
Function: Specific hexamer assembly (Hertel et al.) (irreversible)
Reaction rate: gammap*KaiC_D*(C_P^5)
Kinetic rate constant Value
gammap 5e+4
C_P "KaiC_U" + "KaiC_T" + "KaiC_S" + "KaiC_D"
Details
Equation: KaiC6_D ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_D
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiC6_D -> KaiC_D
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_D
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiC6_D -> KaiC6_T
Function: Mass Action (irreversible)
Reaction rate: ktd*KaiC6_D
Kinetic rate constant Value
ktd "ktdN" + "ktdA" * "Af"
Details
Equation: KaiC6_D -> KaiC6_S
Function: Mass Action (irreversible)
Reaction rate: ksd*KaiC6_D
Kinetic rate constant Value
ksd "ksdN" + "ksdA" * "Af"
Details
Equation: KaiC6_D -> KaiBC_D
Function: Specific protein pool exchange (Hertel et al.) (irreversible)
Reaction rate: cd * KaiC6_D * (KaiC6_D/C_H)^5
Kinetic rate constant Value
cd 2420
C_H "KaiC6_U" + "KaiC6_T" + "KaiC6_S" + "KaiC6_D"
Details
Equation: KaiC_S -> KaiC6_S
Function: Specific hexamer assembly (Hertel et al.) (irreversible)
Reaction rate: gammap*KaiC_S*(C_P^5)
Kinetic rate constant Value
gammap 5e+4
C_P "KaiC_U" + "KaiC_T" + "KaiC_S" + "KaiC_D"
Details
Equation: KaiC6_S ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_S
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiC6_S -> KaiC6_U
Function: Mass Action (irreversible)
Reaction rate: kus*KaiC6_S
Kinetic rate constant Value
kus "kusN" + "kusA" * "Af"
Details
Equation: KaiC6_S -> KaiC_S
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_S
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiC6_S -> KaiC6_D
Function: Mass Action (irreversible)
Reaction rate: kds*KaiC6_S
Kinetic rate constant Value
kds "kdsN" + "kdsA" * "Af"
Details
Equation: KaiC6_S -> KaiBC_S
Function: Specific protein pool exchange (Hertel et al.) (irreversible)
Reaction rate: cs * KaiC6_S * (KaiC6_S/C_H)^5
Kinetic rate constant Value
cs 1380
C_H "KaiC6_U" + "KaiC6_T" + "KaiC6_S" + "KaiC6_D"
Details
Equation: KaiC_T -> KaiC6_T
Function: Specific hexamer assembly (Hertel et al.) (irreversible)
Reaction rate: gammap*KaiC_T*(C_P^5)
Kinetic rate constant Value
gammap 5e+4
C_P "KaiC_U" + "KaiC_T" + "KaiC_S" + "KaiC_D"
Details
Equation: KaiC6_T ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_T
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiC6_T -> KaiC6_U
Function: Mass Action (irreversible)
Reaction rate: kut*KaiC6_T
Kinetic rate constant Value
kut "kutN" + "kutA" * "Af"
Details
Equation: KaiC6_T -> KaiC_T
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_T
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiC6_T -> KaiC6_D
Function: Mass Action (irreversible)
Reaction rate: kdt*KaiC6_T
Kinetic rate constant Value
kdt "kdtN" + "kdtA" * "Af"
Details
Equation: KaiC_U -> KaiC6_U
Function: Specific hexamer assembly (Hertel et al.) (irreversible)
Reaction rate: gammap*KaiC_U*(C_P^5)
Kinetic rate constant Value
gammap 5e+4
C_P "KaiC_U" + "KaiC_T" + "KaiC_S" + "KaiC_D"
Details
Equation: KaiC6_U ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_U
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiC6_U -> KaiC_U
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_U
Kinetic rate constant Value
gammam 0.4
Details
Equation: KaiC6_U -> KaiC6_S
Function: Mass Action (irreversible)
Reaction rate: ksu*KaiC6_U
Kinetic rate constant Value
ksu "ksuN" + "ksuA" * "Af"
Details
Equation: KaiC6_U -> KaiC6_T
Function: Mass Action (irreversible)
Reaction rate: ktu*KaiC6_U
Kinetic rate constant Value
ktu "ktuN" + "ktuA" * "Af"
Details
Equation: KaiC_D ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_D
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiC_S ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_S
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiC_T ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_T
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: KaiC_U ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_U
Kinetic rate constant Value
k4_c 0.0162
Details
Equation: kaiA_mRNA ->
Function: Mass Action (irreversible)
Reaction rate: k3_a*kaiA_mRNA
Kinetic rate constant Value
k3_a 0.0195
Details
Equation: kaiBC_mRNA ->
Function: Mass Action (irreversible)
Reaction rate: k3_bc*kaiBC_mRNA
Kinetic rate constant Value
k3_bc 0.2996
Details
Equation: -> kaiBC_mRNA
Modifiers: KaiC6_U
Function: Specific combined inhibition/activation (Hertel et al.) (irreversible)
Reaction rate: k1_bc*((1+lambda*Zz)/(1+Zz) * 1/(1+KaiC6_U))
Kinetic rate constant Value
k1_bc 0.4139
lambda 3.0378
Zz "KaiC6_T"+ "KaiC6_D"
Details

Constant quantities

Initial expression: 0.0117
Simulation type: fixed
Initial expression: 0.4139
Simulation type: fixed
Initial expression: 3.0378
Simulation type: fixed
Initial expression: 0.3497
Simulation type: fixed
Initial expression: 0.0457
Simulation type: fixed
Initial expression: 0.0195
Simulation type: fixed
Initial expression: 0.2996
Simulation type: fixed
Initial expression: 0.3278
Simulation type: fixed
Initial expression: 0.0162
Simulation type: fixed
Initial expression: 0.01
Simulation type: fixed
Initial expression: 0.13
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 0.22
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 0.34
Simulation type: fixed
Initial expression: 0.12
Simulation type: fixed
Initial expression: 3.9
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 10.9
Simulation type: fixed
Initial expression: 0.6
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 0.5
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 0.6
Simulation type: fixed
Initial expression: 3
Simulation type: fixed
Initial expression: 0.1
Simulation type: fixed
Initial expression: 8e-6
Simulation type: fixed
Initial expression: 0.4
Simulation type: fixed
Initial expression: 5e+4
Simulation type: fixed
Initial expression: 0
Simulation type: fixed
Initial expression: 1380
Simulation type: fixed
Initial expression: 2420
Simulation type: fixed
Initial expression: 3.5
Simulation type: fixed
Initial expression: 0.6
Simulation type: fixed

Assigned quantities

Initial expression: KaiC6_U + KaiC6_T + KaiC6_S + KaiC6_D
Simulation type: assignment
Initial expression: KaiBC_U + KaiBC_T + KaiBC_S + KaiBC_D
Simulation type: assignment
Initial expression: KaiC_U + KaiC_T + KaiC_S + KaiC_D
Simulation type: assignment
Initial expression: KaiC6_T+ KaiC6_D
Simulation type: assignment
Initial expression: C_P + C_H + C_B
Simulation type: assignment
Initial expression: (KaiA + C_total/6 + KDAC)/2 - sqrt((KaiA + C_total/6 + KDAC)^2/4 - KaiA*C_total/6)
Simulation type: assignment
Initial expression: (KaiA-A2C6)/(1 + C_H/KMj + 1/KDAS*(KaiBC_S/6) * (KaiBC_S/C_B)^5)
Simulation type: assignment
Initial expression: kutN + kutA * Af
Simulation type: assignment
Initial expression: kusN + kusA * Af
Simulation type: assignment
Initial expression: ksuN + ksuA * Af
Simulation type: assignment
Initial expression: ktuN + ktuA * Af
Simulation type: assignment
Initial expression: ktdN + ktdA * Af
Simulation type: assignment
Initial expression: kdtN + kdtA * Af
Simulation type: assignment
Initial expression: ksdN + ksdA * Af
Simulation type: assignment
Initial expression: kdsN + kdsA * Af
Simulation type: assignment
Name Value
cytosol 1
kaiA_mRNA 0
kaiBC_mRNA 0
KaiA 2*AT
KaiC6_U 0.998*CT
KaiC6_T 0.001*CT
KaiC6_S 0
KaiC6_D 0
KaiBC_U 0.001*CT
KaiBC_T 0
KaiBC_S 0
KaiBC_D 0
KaiC_U 0
KaiC_T 0
KaiC_S 0
KaiC_D 0

Constant quantities

Name Value
k1_a 0.0117
k1_bc 0.4139
lambda 3.0378
k2_a 0.3497
k2_bc 0.0457
k3_a 0.0195
k3_bc 0.2996
k4_a 0.3278
k4_c 0.0162
ktuN 0.01
kdtN 0.13
kdsN 0
ksuN 0
kutN 0.22
ktdN 0
ksdN 0.34
kusN 0.12
ktuA 3.9
kdtA 0
kdsA 10.9
ksuA 0.6
kutA 0
ktdA 0.5
ksdA 0
kusA 0.6
KMj 3
KDAC 0.1
KDAS 8e-6
gammam 0.4
gammap 5e+4
cu 0
cs 1380
cd 2420
CT 3.5
AT 0.6

Assigned quantities

Name Value
C_H KaiC6_U + KaiC6_T + KaiC6_S + KaiC6_D
C_B KaiBC_U + KaiBC_T + KaiBC_S + KaiBC_D
C_P KaiC_U + KaiC_T + KaiC_S + KaiC_D
Zz KaiC6_T+ KaiC6_D
C_total C_P + C_H + C_B
A2C6 (KaiA + C_total/6 + KDAC)/2 - sqrt((KaiA + C_total/6 + KDAC)^2/4 - KaiA*C_total/6)
Af (KaiA-A2C6)/(1 + C_H/KMj + 1/KDAS*(KaiBC_S/6) * (KaiBC_S/C_B)^5)
kut kutN + kutA * Af
kus kusN + kusA * Af
ksu ksuN + ksuA * Af
ktu ktuN + ktuA * Af
ktd ktdN + ktdA * Af
kdt kdtN + kdtA * Af
ksd ksdN + ksdA * Af
kds kdsN + kdsA * Af
Name Value
end time 250  
start time 0  
time offset 0  

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