Install From Binaries

note

At the moment, static binaries are only available through the GUI.

Graphical User Interface

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

Download

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

MacOS Arm64

Download

permissions

Right-Click > Open > Ok

MacOS Intel

Download

permissions

Right-Click > Open > Ok

Linux

Download

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!

To understand how the Spatial Model Editor uses DuneCopasi, visit the GUI usage documentation.