Usage - HelikarLab/ode-app GitHub Wiki

Please visit http://kinode.herokuapp.com/ to use the application.

General functions

Import a SBML model

Only .sbml/.xml files supported

Import Model Demo

Use a saved model

Saved Models Demo

Model Tab

View Reactions/Species of a model

Click on a reaction/specie to view it on the info panel.

View Reaction/Specie Demo

View the model visualized in a network graph

Drag and zoom on the graph panel. You can also switch the compartments to display compartment-wise reactions and species.

  • Blue Circles -> Specie Nodes
  • Red Circles -> Reaction Nodes
  • Green line -> Reactant Edge
  • Yellow line -> Product Edge
  • Dotted line -> Reversible reactions

Graph Demo

Save a model

Saving a model stores it in the database which will let you directly fetch it later without doing an import.

Save Model Demo

Simulation Tab

Perform a simple simulation

Follow the gif 😉. All simulations are governed by Kinetic Laws.

Simulation Demo

View the result in the plot with additional features

Play around with the plot panel.

Plot Demo

Toggle a specie from the plot

Toggle Demo

Download the plot

Download Demo