Spatial Model Editor
The Spatial Model Editor (SME) is a user friendly GUI editor to create and edit 2D and 3D spatial Systems Biology Markup Language (SBML) models of bio-chemical reactions. Additionally, it can run simulations with DuneCopasi. A big adventage of this package is that is tailored for biologists and is available with just a click on the major plataforms. You can download it here:
- Windows
- MacOS Arm64
- MacOS Intel
- Linux
permissions
chmod +x spatial-model-editor
Fedora/RHEL/CentOS
On linux some additional system libraries are required that may not be installed by default. To install them:
sudo yum install xcb-util-image xcb-util-keysyms xcb-util-renderutil xcb-util-wm
permissions
Right-Click > Open > Ok
permissions
Right-Click > Open > Ok
permissions
More info > Run anyway
Or take a look at the Spatial Model Editor (SME) website or its documentation. Note that the version of DuneCopasi and the Spatial Model Editor are not synchronized!