Model repository

Models

Miyoshi et al. 2007

Plyusnina et al. (in prep.)

Hertel et al. 2013

Jablonsky et al. 2014

Grimaud et al. 2014

E-cyano team 2017, clock & C-N metabolism

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.

Fridlyand et al. 1995

Fridlyand L, Kaplan A, Reinhold L (1995) Quantitative evaluation of the role of a putative CO2-scavenging entity in the cyanobacterial CO2-concentrating mechanism. Biosystems 1996;37(3):229-38.

model:Fridlyand et al. (1995)

This paper assesses the contribution of a postulated CO2-scavenging system to the efficient operation of the CO2-concentrating mechanism (CCM) in cyanobacteria. A quantitative model for the CCM is presented which incorporates an energy-dependent carbonic anhydrase-like entity located at or near the inner surface of the plasma membrane. This entity, which converts CO2 to HCO3- against the thermodynamic potential, scavenges CO2 leaking outward from the carboxysomes, and, further, converts CO2 entering from the medium to HCO3-, thus maintaining an inward diffusion gradient along which CO2 enters passively. The model resembles our earlier models in postulating that CO2 and HCO3- are not at equilibrium throughout the greater part of the cell, and that CO2 is generated in high concentration at carbonic anhydrase sites within the carboxysomes. The model further takes into account the concentric thylakoid membranes which surround the carboxysomes, and events in the periplasmic space and the unstirred layer surrounding the cell. Implications of the predicted steady state fluxes of CO2 and HCO3-, and of their steady state concentrations in various cellular compartments, are discussed. The plasma membrane carbonic anhydrase-like activity lowers the photosynthetic Km for external Ci, as well as decreasing the inorganic C 'leak', but it may not save on energy expenditure.

model:Fridlyand et al. (1995)

publication:Fridlyand et al. (1995)

Fridlyand L, Kaplan A, Reinhold L (1995) Quantitative evaluation of the role of a putative CO2-scavenging entity in the cyanobacterial CO2-concentrating mechanism. Biosystems 1996;37(3):229-38.

publication:Fridlyand et al. (1995)

Contains:

carb