spatial-model-editor

Getting started

  • Setting the stage
  • Find your bearings
  • Importing Geometry
  • Assign Compartments
  • Mesh generation
  • Species properties
  • Defining reactions
  • Defining parameters
  • Defining additional functions
  • Running a Simulation

Example models

  • Overview
  • Single compartment diffusion
  • AB-to-C Reaction model
  • Gray Scott
  • A very simple model
  • Brusselator model
  • Liver cells
  • Circadian clock
  • Simplified liver model
  • Sel’Kov Model
  • FitzHugh-Nagumo
  • Calcium-Wave-Propagation Model

User guides

  • Work with SBML and COPASI models
  • How to create your own geometry

Python interface

  • Python Interface
  • Example Notebooks
  • API Reference

Reference documentation

  • dune-copasi simulator
  • Pixel simulator
  • Parameter optimization
  • Steady state analysis
  • Mesh generation
  • Command Line Interface
  • Maths
  • Units
  • Changelog
  • Source Code
  • License

Developer documentation

  • Core
  • Pixel
  • Tests
  • Documentation
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© Copyright 2019, Liam Keegan.

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