Simbiotics is a 3D simulation tool offering a range of modelling features to describe bacterial populations. Bacterial cells are represented as discrete geometric entities which may have internal processes and interact with their environment. Modellers may describe specific bacterial behaviour, environmental factors and the spatial arrangement of cellular populations, this is achieved via composing library modules into a model specification. Modules describe specific features to be simulated and are parameterisable, the library is extendable to allow for novel models of relevant processes to be added to the tool. Simulations can be run on mulit-threaded and multi-CPU environments to ensure the platform can represent industrially relevant systems.
Simbiotics can be initialised via common standards experimentalists use such as microscopy image data and SBML models, allowing for the rapid development of 3D population models. An optional live 3D rendering and data graphing is available, alternatively exporting data in common formats (CSV and JSON) allow for the integration of Simbiotics into existing tools such as Blender or PovRay. The tool requires minimal programming experience to use.
To learn how to run and configure Simbiotics, read the user manual.
You can download the Simbiotics Java source code (GNU GPLv3).
If you use Simbiotics, please cite the following publication: