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Model repository

Models

+ Miyoshi et al. 2007
+ Plyusnina et al. (in prep.)
+ Hertel et al. 2013
+ Jablonsky et al. 2014
+ Clark et al. 2014 (in progress)
+ Fridlyand et al. 1995
o Grimaud et al. 2014
o E-cyano team 2017, clock & C-N metabolism
o Müller et al. 2019

Navigation
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.

Annotations Tab
All the annotation terms relevant for the currently focused level of the project are displayed on the Annotation Tab below the scheme. Individual annotation data can be unfolded by clicking on the requested annotation item header.

Components Tab
The Components Tab displays all the model species (state variables). More information for particular components are accessible after clicking on the requested component header.

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.

Simulation Tab
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.

Analysis Tab
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.

Annotations
Components
Reactions
Parameters
Simulation
Analysis
Experiments
+publication: 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.


publication: Hertel et al. 2013
Contains:
+cytosol
Initial expression: 1
Simulation type: fixed
Details
+kaiA_mRNA
Initial expression: 0
Simulation type: reaction
Details
+kaiBC_mRNA
Initial expression: 0
Simulation type: reaction
Details
+KaiA
Initial expression: 2*AT
Simulation type: reaction
Details
+KaiC6_U
Initial expression: 0.998*CT
Simulation type: reaction
Details
+KaiC6_T
Initial expression: 0.001*CT
Simulation type: reaction
Details
+KaiC6_S
Initial expression: 0
Simulation type: reaction
Details
+KaiC6_D
Initial expression: 0
Simulation type: reaction
Details
+KaiBC_U
Initial expression: 0.001*CT
Simulation type: reaction
Details
+KaiBC_T
Initial expression: 0
Simulation type: reaction
Details
+KaiBC_S
Initial expression: 0
Simulation type: reaction
Details
+KaiBC_D
Initial expression: 0
Simulation type: reaction
Details
+KaiC_U
Initial expression: 0
Simulation type: reaction
Details
+KaiC_T
Initial expression: 0
Simulation type: reaction
Details
+KaiC_S
Initial expression: 0
Simulation type: reaction
Details
+KaiC_D
Initial expression: 0
Simulation type: reaction
Details
+KaiA degradation
Equation: KaiA ->
Function: Mass Action (irreversible)
Reaction rate: k4_a*KaiA
Kinetic rate constant Value
k4_a 0.3278
Details
+KaiA translation
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
+KaiA_mRNA transcription
Equation: -> kaiA_mRNA
Function: General flux (reversible)
Reaction rate: k1_a
Kinetic rate constant Value
k1_a 0.0117
Details
+KaiBC_D degradation
Equation: KaiBC_D ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_D
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiBC_D dissociation
Equation: KaiBC_D -> KaiC_D
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_D
Kinetic rate constant Value
gammam 0.4
Details
+KaiBC_D serine dephosphorylation
Equation: KaiBC_D -> KaiBC_S
Function: Mass Action (irreversible)
Reaction rate: ksdN*KaiBC_D
Kinetic rate constant Value
ksdN 0.34
Details
+KaiBC_D threonine dephosphorylation
Equation: KaiBC_D -> KaiBC_T
Function: Mass Action (irreversible)
Reaction rate: ktdN*KaiBC_D
Kinetic rate constant Value
ktdN 0
Details
+KaiBC_S degradation
Equation: KaiBC_S ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_S
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiBC_S dephoshporylation
Equation: KaiBC_S -> KaiBC_U
Function: Mass Action (irreversible)
Reaction rate: kusN*KaiBC_S
Kinetic rate constant Value
kusN 0.12
Details
+KaiBC_S dissociation
Equation: KaiBC_S -> KaiC_S
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_S
Kinetic rate constant Value
gammam 0.4
Details
+KaiBC_S threonine phosphorylation
Equation: KaiBC_S -> KaiBC_D
Function: Mass Action (irreversible)
Reaction rate: kdsN*KaiBC_S
Kinetic rate constant Value
kdsN 0
Details
+KaiBC_T degradation
Equation: KaiBC_T ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_T
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiBC_T dephosphorylation
Equation: KaiBC_T -> KaiBC_U
Function: Mass Action (irreversible)
Reaction rate: kutN*KaiBC_T
Kinetic rate constant Value
kutN 0.22
Details
+KaiBC_T dissociation
Equation: KaiBC_T -> KaiC_T
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_T
Kinetic rate constant Value
gammam 0.4
Details
+KaiBC_T serine phosphorylation
Equation: KaiBC_T -> KaiBC_D
Function: Mass Action (irreversible)
Reaction rate: kdtN*KaiBC_T
Kinetic rate constant Value
kdtN 0.13
Details
+KaiBC_U degradation
Equation: KaiBC_U ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiBC_U
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiBC_U dissociation
Equation: KaiBC_U -> KaiC_U
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiBC_U
Kinetic rate constant Value
gammam 0.4
Details
+KaiBC_U serine phosphorylation
Equation: KaiBC_U -> KaiBC_S
Function: Mass Action (irreversible)
Reaction rate: ksuN*KaiBC_U
Kinetic rate constant Value
ksuN 0
Details
+KaiBC_U threonine phosphorylation
Equation: KaiBC_U -> KaiBC_T
Function: Mass Action (irreversible)
Reaction rate: ktuN*KaiBC_U
Kinetic rate constant Value
ktuN 0.01
Details
+KaiBC_U to KaiC6_U exchange
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
+KaiC translation
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
+KaiC6_D assembly
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
+KaiC6_D degradation
Equation: KaiC6_D ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_D
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiC6_D dissociation
Equation: KaiC6_D -> KaiC_D
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_D
Kinetic rate constant Value
gammam 0.4
Details
+KaiC6_D serine dephoshorylation
Equation: KaiC6_D -> KaiC6_T
Function: Mass Action (irreversible)
Reaction rate: ktd*KaiC6_D
Kinetic rate constant Value
ktd "ktdN" + "ktdA" * "Af"
Details
+KaiC6_D threonine dephoshorylation
Equation: KaiC6_D -> KaiC6_S
Function: Mass Action (irreversible)
Reaction rate: ksd*KaiC6_D
Kinetic rate constant Value
ksd "ksdN" + "ksdA" * "Af"
Details
+KaiC6_D to KaiBC_D exchange
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
+KaiC6_S assembly
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
+KaiC6_S degradation
Equation: KaiC6_S ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_S
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiC6_S dephosphorylation
Equation: KaiC6_S -> KaiC6_U
Function: Mass Action (irreversible)
Reaction rate: kus*KaiC6_S
Kinetic rate constant Value
kus "kusN" + "kusA" * "Af"
Details
+KaiC6_S dissociation
Equation: KaiC6_S -> KaiC_S
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_S
Kinetic rate constant Value
gammam 0.4
Details
+KaiC6_S threonine phosphorylation
Equation: KaiC6_S -> KaiC6_D
Function: Mass Action (irreversible)
Reaction rate: kds*KaiC6_S
Kinetic rate constant Value
kds "kdsN" + "kdsA" * "Af"
Details
+KaiC6_S to KaiBC_S exchange
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
+KaiC6_T assembly
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
+KaiC6_T degradation
Equation: KaiC6_T ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_T
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiC6_T dephosphorylation
Equation: KaiC6_T -> KaiC6_U
Function: Mass Action (irreversible)
Reaction rate: kut*KaiC6_T
Kinetic rate constant Value
kut "kutN" + "kutA" * "Af"
Details
+KaiC6_T dissociation
Equation: KaiC6_T -> KaiC_T
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_T
Kinetic rate constant Value
gammam 0.4
Details
+KaiC6_T serine phosphorylation
Equation: KaiC6_T -> KaiC6_D
Function: Mass Action (irreversible)
Reaction rate: kdt*KaiC6_T
Kinetic rate constant Value
kdt "kdtN" + "kdtA" * "Af"
Details
+KaiC6_U assembly
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
+KaiC6_U degradation
Equation: KaiC6_U ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC6_U
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiC6_U dissociation
Equation: KaiC6_U -> KaiC_U
Function: Mass Action (irreversible)
Reaction rate: gammam*KaiC6_U
Kinetic rate constant Value
gammam 0.4
Details
+KaiC6_U serine phosphorylation
Equation: KaiC6_U -> KaiC6_S
Function: Mass Action (irreversible)
Reaction rate: ksu*KaiC6_U
Kinetic rate constant Value
ksu "ksuN" + "ksuA" * "Af"
Details
+KaiC6_U threnine phosphorylation
Equation: KaiC6_U -> KaiC6_T
Function: Mass Action (irreversible)
Reaction rate: ktu*KaiC6_U
Kinetic rate constant Value
ktu "ktuN" + "ktuA" * "Af"
Details
+KaiC_D degradation
Equation: KaiC_D ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_D
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiC_S degradation
Equation: KaiC_S ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_S
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiC_T degradation
Equation: KaiC_T ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_T
Kinetic rate constant Value
k4_c 0.0162
Details
+KaiC_U degradation
Equation: KaiC_U ->
Function: Mass Action (irreversible)
Reaction rate: k4_c*KaiC_U
Kinetic rate constant Value
k4_c 0.0162
Details
+kaiA_mRNA degradation
Equation: kaiA_mRNA ->
Function: Mass Action (irreversible)
Reaction rate: k3_a*kaiA_mRNA
Kinetic rate constant Value
k3_a 0.0195
Details
+kaiBC_mRNA degradation
Equation: kaiBC_mRNA ->
Function: Mass Action (irreversible)
Reaction rate: k3_bc*kaiBC_mRNA
Kinetic rate constant Value
k3_bc 0.2996
Details
+kaiBC_mRNA transcription
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

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

Assigned quantities

+C_H
Initial expression: KaiC6_U + KaiC6_T + KaiC6_S + KaiC6_D
Simulation type: assignment
+C_B
Initial expression: KaiBC_U + KaiBC_T + KaiBC_S + KaiBC_D
Simulation type: assignment
+C_P
Initial expression: KaiC_U + KaiC_T + KaiC_S + KaiC_D
Simulation type: assignment
+Zz
Initial expression: KaiC6_T+ KaiC6_D
Simulation type: assignment
+C_total
Initial expression: C_P + C_H + C_B
Simulation type: assignment
+A2C6
Initial expression: (KaiA + C_total/6 + KDAC)/2 - sqrt((KaiA + C_total/6 + KDAC)^2/4 - KaiA*C_total/6)
Simulation type: assignment
+Af
Initial expression: (KaiA-A2C6)/(1 + C_H/KMj + 1/KDAS*(KaiBC_S/6) * (KaiBC_S/C_B)^5)
Simulation type: assignment
+kut
Initial expression: kutN + kutA * Af
Simulation type: assignment
+kus
Initial expression: kusN + kusA * Af
Simulation type: assignment
+ksu
Initial expression: ksuN + ksuA * Af
Simulation type: assignment
+ktu
Initial expression: ktuN + ktuA * Af
Simulation type: assignment
+ktd
Initial expression: ktdN + ktdA * Af
Simulation type: assignment
+kdt
Initial expression: kdtN + kdtA * Af
Simulation type: assignment
+ksd
Initial expression: ksdN + ksdA * Af
Simulation type: assignment
+kds
Initial expression: kdsN + kdsA * Af
Simulation type: assignment
+Initial conditions
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
+Parameters

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
+Options
Name Value
end time 250  
start time 0  
time offset 0  

Simulate   Export sbml

Conservation analysis

Conservation

Modes analysis

Modes

Matrix analysis

Matrix
Please use the following reference to cite this web site:
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI