## Models

**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.

## 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.

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**

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:**

**Initial expression:**1

**Simulation type:**fixed

**Initial expression:**Nf+Nr

**Simulation type:**assignment

**Initial expression:**Cf+Cr+Cnit

**Simulation type:**assignment

**Initial expression:**Cf*alpha3

**Simulation type:**assignment

**Initial expression:**0

**Dynamic expression:**r4*phi*Cf - (r7 + D_)*Cnit

**Simulation type:**ode

**Initial expression:**100

**Dynamic expression:**2*r1*Cnit - (alpha3*r3*Cr/Nf+lambda6*r1*Cnit/Nf + D_)*Nr

**Simulation type:**ode

**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

**Initial expression:**650

**Dynamic expression:**r3*Cr*Nr/Nf - (r4*phi+D_)*Cf + r7*Cnit

**Simulation type:**ode

**Initial expression:**0

**Dynamic expression:**1

**Simulation type:**ode

#### Constant quantities

**Initial expression:**8

**Simulation type:**fixed

**Initial expression:**0.0001

**Simulation type:**fixed

**Initial expression:**24

**Simulation type:**fixed

**Initial expression:**6

**Simulation type:**fixed

**Initial expression:**1

**Simulation type:**fixed

**Initial expression:**0

**Simulation type:**fixed

**Initial expression:**0.08

**Simulation type:**fixed

**Initial expression:**0.27

**Simulation type:**fixed

**Initial expression:**4500

**Simulation type:**fixed

**Initial expression:**55.5

**Simulation type:**fixed

**Initial expression:**0.88

**Simulation type:**fixed

**Initial expression:**0.0083

**Simulation type:**fixed

**Initial expression:**5200

**Simulation type:**fixed

**Initial expression:**0.4

**Simulation type:**fixed

**Initial expression:**0.155

**Simulation type:**fixed

**Initial expression:**1.9

**Simulation type:**fixed

**Initial expression:**0.027

**Simulation type:**fixed

**Initial expression:**0.83

**Simulation type:**fixed

**Initial expression:**9.3e-4

**Simulation type:**fixed

**Initial expression:**0.023

**Simulation type:**fixed

**Initial expression:**0.275

**Simulation type:**fixed

**Initial expression:**14.5

**Simulation type:**fixed

#### Assigned quantities

**Initial expression:**theta0+theta1/2*((1+tanh(t2/Tj))-(1+tanh((t2-Tp)/Tj))+(1+tanh((t2-Tc)/Tj)))

**Simulation type:**assignment

**Initial expression:**130/3/3

**Simulation type:**assignment

**Initial expression:**130*exp(1)^(-1*(((mod((time+6),24))-6)^2)/(2*2^2))/3

**Simulation type:**assignment

**Initial expression:**mod((time+6+phase),Tc)

**Simulation type:**assignment

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