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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

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

Grimaud et al. 2014

A dynamical model that describes the daily dynamics of diazotrophy in a unicellular cyanobacterium, Crocosphaera watsonii WH8501, in regard to light limitation and obligate diazotrophy.

Annotations
Components
Reactions
Parameters
Simulation
Analysis
Experiments
+model: Grimaud et al. 2014

A dynamical model is proposed that describes the daily dynamics of diazotrophy in a unicellular cyanobacterium, Crocosphaera watsonii WH8501, in regard to light limitation and obligate diazotrophy. In this model, intracellular carbon and nitrogen are both divided into a functional pool and a storage pool. Aninternal pool that explicitly describes the nitrogenase enzyme is also added. The various intracellularcarbon and nitrogen flows between these pools lead to a complex dynamics driven by the light regime.The model is successfully validated with continuous cultures experiments of C. watsonii under three lightregimes, indicating that the proposed mechanisms accurately reproduce the growth dynamics of thisorganism under various light environments. Then, a series of model simulations is run for a range of lightregimes with different photoperiods and daily light doses. Results reveal how nitrogen and carbon arecoupled, through the diel cycle, along with nitrogenase dynamics whose activity is constrained by thelight regime. In an ecological perspective, we picture the effect of such irradiance condition on growthand on the carbon to nitrogen stoichiometry on cells. This model could prove useful to understand thelatitudinal distribution of this cyanobacterium in the global ocean.


model: Grimaud et al. 2014
+publication: model Grimaud et al. 2014

Grimaud, G. M., Rabouille, S., Dron, A., Sciandra, A., & Bernard, O. (2014). Modelling the dynamics of carbon–nitrogen metabolism in the unicellular diazotrophic cyanobacterium Crocosphaera watsonii WH8501, under variable light regimes. Ecological modelling, 291, 121-133.


publication: model Grimaud et al. 2014
Contains:
+Cytosol
Initial expression: 1
Simulation type: fixed
+Ntot
Initial expression: Nf+Nr
Simulation type: assignment
+Ctot
Initial expression: Cf+Cr+Cnit
Simulation type: assignment
+Nf
Initial expression: Cf*alpha3
Simulation type: assignment
+Cnit
Initial expression: 0
Dynamic expression: r4*phi*Cf - (r7 + D_)*Cnit
Simulation type: ode
+Nr
Initial expression: 100
Dynamic expression: 2*r1*Cnit - (alpha3*r3*Cr/Nf+lambda6*r1*Cnit/Nf + D_)*Nr
Simulation type: ode
+Cr
Initial expression: 100
Dynamic expression: r2*(Ir/(Ir+Kl+I_*I_/Kil))*Cf - ((r3+r3*gamma3)*Nr/Nf + r5 + D_)*Cr- alpha1*r1*Cnit - lambda5*(r2*(Ir/(Ir+Kl+I_*I_/Kil))*Cf)/Cf*Cnit
Simulation type: ode
+Cf
Initial expression: 650
Dynamic expression: r3*Cr*Nr/Nf - (r4*phi+D_)*Cf + r7*Cnit
Simulation type: ode
+time
Initial expression: 0
Dynamic expression: 1
Simulation type: ode

Constant quantities

+phase
Initial expression: 8
Simulation type: fixed
+Tj
Initial expression: 0.0001
Simulation type: fixed
+Tc
Initial expression: 24
Simulation type: fixed
+Tp
Initial expression: 6
Simulation type: fixed
+theta1
Initial expression: 1
Simulation type: fixed
+theta0
Initial expression: 0
Simulation type: fixed
+Kb
Initial expression: 0.08
Simulation type: fixed
+k_
Initial expression: 0.27
Simulation type: fixed
+Kil
Initial expression: 4500
Simulation type: fixed
+Kl
Initial expression: 55.5
Simulation type: fixed
+lambda6
Initial expression: 0.88
Simulation type: fixed
+D_
Initial expression: 0.0083
Simulation type: fixed
+lambda5
Initial expression: 5200
Simulation type: fixed
+gamma3
Initial expression: 0.4
Simulation type: fixed
+alpha3
Initial expression: 0.155
Simulation type: fixed
+alpha1
Initial expression: 1.9
Simulation type: fixed
+r5
Initial expression: 0.027
Simulation type: fixed
+r7
Initial expression: 0.83
Simulation type: fixed
+r4
Initial expression: 9.3e-4
Simulation type: fixed
+r3
Initial expression: 0.023
Simulation type: fixed
+r2
Initial expression: 0.275
Simulation type: fixed
+r1
Initial expression: 14.5
Simulation type: fixed

Assigned quantities

+phi
Initial expression: theta0+theta1/2*((1+tanh(t2/Tj))-(1+tanh((t2-Tp)/Tj))+(1+tanh((t2-Tc)/Tj)))
Simulation type: assignment
+I_
Initial expression: 130/3/3
Simulation type: assignment
+Ir
Initial expression: 130*exp(1)^(-1*(((mod((time+6),24))-6)^2)/(2*2^2))/3
Simulation type: assignment
+t2
Initial expression: mod((time+6+phase),Tc)
Simulation type: assignment
+Initial conditions
Name Value
Cytosol 1
Ntot Nf+Nr
Ctot Cf+Cr+Cnit
Nf Cf*alpha3
Cnit 0
Nr 100
Cr 100
Cf 650
time 0
+Parameters

Constant quantities

Name Value
phase 8
Tj 0.0001
Tc 24
Tp 6
theta1 1
theta0 0
Kb 0.08
k_ 0.27
Kil 4500
Kl 55.5
lambda6 0.88
D_ 0.0083
lambda5 5200
gamma3 0.4
alpha3 0.155
alpha1 1.9
r5 0.027
r7 0.83
r4 9.3e-4
r3 0.023
r2 0.275
r1 14.5

Assigned quantities

Name Value
phi theta0+theta1/2*((1+tanh(t2/Tj))-(1+tanh((t2-Tp)/Tj))+(1+tanh((t2-Tc)/Tj)))
I_ 130/3/3
Ir 130*exp(1)^(-1*(((mod((time+6),24))-6)^2)/(2*2^2))/3
t2 mod((time+6+phase),Tc)
+Options
Name Value
Simulation End 200  
Simulation Start 0  
Simulation Steps 2000  

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