ingallslab / bsim

BSim

BSim is an agent-based modelling tool designed to allow for the study of bacterial populations. By enabling the description of bacterial behaviours, it attempts to provide an environment in which to investigate how local interactions between individual bacterium leads to the emergence of population level features, such as cooperation and synchronisation.

Case studies

Emergent oscillations in a synthetic multicellular consortium

We adapted the model from Chen et al., Science, 2015 (DOI: 10.1126/science.aaa3794).

The code for this case study can be found here.

A video of an example simulation can be found here: https://www.youtube.com/watch?v=FpG7EgIC5yI

Consortium controller

The implementation of the model from our paper 'In-Silico Analysis and Implementation of a Multicellular Feedback Control Strategy in a Synthetic Bacterial Consortium' (Fiore G, Matyjaszkiewicz A, et al., ACS Synth. Biol., 2017; DOI: 10.1021/acssynbio.6b00220).

Code for this example can be found here. Further instructions for running the code can be found in the README.md located in the above directory.

A video of an example simulation can be found here: https://www.youtube.com/watch?v=wBLXv9znhqE

Building and running

BSim can be built and run from your favourite IDE (e.g., IntelliJ IDEA, eclipse, ...); see below for further details.

Alternatively, the whole source tree can be build from the command line using Ant:

ant -f bsim-build-tree.xml

The resulting compiled classes will reside in the directory ./out/*.

Using an IDE

IntelliJ IDEA

1. Clone this repository.
2. Open the cloned repository directory as a new project in IntelliJ.
3. In the project structure pane, right click each source directory (src, examples, and test) and select Mark Directory as -> Sources Root for each directory.
4. In the project structure pane, right click the lib directory and select Add as Library.
5. You may need to set the project SDK (your installed Java JDK) and output path (./out). This can be done from File -> Project Structure -> Project Settings -> Project.

Eclipse

See here for details.

Citing BSim

If you have made use of BSim in academic or commercial work, the project can be referenced using the following paper(s):

• The latest version of BSim: Matyjaszkiewicz A, Fiore G, et al. (2017) BSim 2.0: An Advanced Agent-Based Cell Simulator. ACS Synthetic Biology (web)Article ASAP doi:10.1021/acssynbio.7b00121

• The original article describing BSim: Gorochowski TE, Matyjaszkiewicz A, Todd T, Oak N, Kowalska K, et al. (2012) BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology. PLoS ONE 7(8): e42790. doi:10.1371/journal.pone.0042790