Specification

Based on the requirements of kinetic metabolic modeling, we identified a set of steps necessary to be followed during model construction, in particular, for large-scale networks. These include:

1. model reduction;
2. adding automatically the initial metabolite concentrations and flux data values into rate equations according to each reaction;
3. generating automatically approximated rate equations based on the stoichiometric matrix of the network;
4. model simulation.

The goal is to facilitate the use of tools so as to help system biologysist, when they perform computational research. To use these tools, upload the input file(s) and click on the corresponding button. When the job has finished click "save" to download the file.
Note that the metabolites and flux names in the text files should coincide with the ID names included in the SBML file.

Model reduction

Reduce the model based on the conjunctive method, as described in the paper [1] .

:  see example file 1

OR
SBML from database: show files

hide files

:  see example file 2

OR
load Fluxes from database: show files

hide files

:  see example




Add metabolites

Set automatically the initial metabolite values for all metabolites in the SBML model.

:  see example file 1

OR
SBML from database: show files

hide files

:  see example file 2

OR
load Metabolites from database: show files

hide files



Translate kinetic equations

Convert metabolic network into kinetic model. Generate automatically approximate kinetic rate laws for all reactions based on the stoichiometry of the network in SBML format.

:  see example file

OR
SBML from database: show files

hide files

:




Add fluxes

Set automatically the flux values of the rate reactions in the SBML model.

:  see example file 1

OR
SBML from database: show files

hide files

:  see example file 2

OR
load Fluxes from database: show files

hide files



Model simulation

It is possible to simulate the SBML kinetic models present in the repository, or an uploaded SBML model.


There are three simulations available:

  • Time-course simulation for metabolites
  • Time-course simulation for reaction fluxes
  • Steady-state


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