Spatial Model Editor Documentation

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
  • sme-contrib
• Example Notebooks
  • Getting started
  • Simulating
  • Visualization
• API Reference
  • sme

Reference documentation

• dune-copasi simulator
  • Simulation options
• Pixel simulator
  • Simulation options
  • Spatial discretization
  • Time integration
  • Adaptive timestep
  • Maximum timestep
  • Boundary Conditions
• Parameter optimization
  • Optimization Setup
  • Optimization Parameter
  • Optimization Target
  • Optimization Target Image Import
  • More information
• Steady state analysis
  • Settings for steady state solvers
  • Solver controls
• Mesh generation
  • Pixel contours
  • Pixel-Edge contours
  • Boundary line simplification
  • Interior points
  • Triangulation
  • Mesh refinement
• Command Line Interface
  • Simulation
  • Parameter fitting
  • Command line parameters
  • Using a config file
• Maths
  • Reaction-Diffusion
  • Compartment Reactions
  • Membrane reactions
  • Boundary Conditions
• Units
  • Fundamental Units
  • Derived Units
  • More information
• Changelog
  • [1.11.0] - 2026-02-04
  • [1.10.1] - 2025-12-03
  • [1.10.0] - 2025-11-20
  • [1.9.0] - 2025-03-31
  • [1.8.0] - 2025-01-29
  • [1.7.0] - 2024-10-29
  • [1.6.0] - 2024-03-26
  • [1.5.0] - 2023-12-01
  • [1.4.0] - 2023-09-04
  • [1.3.6] - 2023-05-23
  • [1.3.5] - 2023-03-02
  • [1.3.4] - 2023-02-23
  • [1.3.3] - 2022-12-05
  • [1.3.2] - 2022-10-13
  • [1.3.1] - 2022-08-10
  • [1.3.0] - 2022-06-10
  • [1.2.2] - 2022-04-28
  • [1.2.1] - 2021-09-30
  • [1.2.0] - 2021-09-13
  • [1.1.5] - 2021-09-01
  • [1.1.4] - 2021-08-17
  • [1.1.3] - 2021-08-10
  • [1.1.2] - 2021-07-13
  • [1.1.1] - 2021-05-30
  • [1.1.0] - 2021-05-04
  • [1.0.9] - 2021-04-06
  • [1.0.8] - 2021-02-10
  • [1.0.7] - 2021-02-07
  • [1.0.6] - 2021-01-29
  • [1.0.5] - 2021-01-02
  • [1.0.4] - 2020-10-22
  • [1.0.3] - 2020-10-19
  • [1.0.2] - 2020-10-16
  • [1.0.1] - 2020-10-5
  • [1.0.0] - 2020-10-2
• Source Code
• License

Developer documentation

• Core
  • sme::model
  • sme::mesh
  • sme::simulate
  • sme::common
• Tests
  • Diffusion