Funded project, 2023Spatial Model Editor

Spatial Model Editor provides a user friendly GUI editor to create and edit spatial SBML models of bio-chemical reactions and simulate them using the dune-copasi solver for reaction-diffusion systems. The goal of this project is to extend the software from two-dimensional to three-dimensional spatial models, which involves multiple aspects including image segmentation, meshing, PDEs and SBML.

• Added support for import and export of 3d SBML models
• Extended Pixel solver to support 3d and anisotropic voxels
• In progress: Automatic segmentation and meshing of voxel geometry
• In progress: Visualization of generated 3d meshes