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Model repository

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.

Müller et al. 2019

Constant quantities

Assigned quantities

Name Value

Constant quantities

Name Value

Assigned quantities

Name Value
Name Value

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