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GUI spatial model editor
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README.md

Spatial Model Editor

github releases linux/osx build status windows build status codecov sonarcloud quality gate status documentation status

A GUI editor to convert non-spatial SBML models of bio-chemical reactions into 2d spatial models and simulate them using the dune-copasi solver for reaction-diffusion systems.

linux executable mac executable windows executable documentation

screenshot

Project status

WP1a

Allow the user to describe a spatial model: import/export SBML, add geometry, diffusion coefficients, spatially varying initial concentrations, etc.

WP1b

Translate the spatial model to a system of PDEs and simulate it: generate 2d triangular mesh, construct PDEs and Jacobians, simulate using DUNE, visualize simulation results, etc.

Implementation details

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