Simbiotics

Simbiotics is a simulation tool for modelling populations of interacting cells. It implements common processes in multicellular populations, focusing on the dynamics of bacteria. Cells are represented as discrete geometric entities which may have internal processes and interact with their environment. Modellers can design their system of interest by attaching library modules to a model specification, defining the cell behaviours, environmental factors, and the initial spatial arrangement of cells and chemicals. The library contains a range of bacterial behaviour modules that allows for the modelling of processes such as gene regulation, cell growth, active motility, gene transfer and many more.

Simbiotics can run single-cell models using differential equations, Gillespie simulations, SBML simulations and boolean networks. It can also simulate extracellular diffusion to allow for communication between the cells. Simulations can be run in multi-threaded and multi-CPU environments to improve performance. The library is extendable and adding novel models of relevant processes is possible.

Easybiotics is a graphical user environment for developing, running and analysing Simbiotics models. To use, it does not require any programming knowledge, the models can be build through "click and select" interfaces. It allows for rapid prototyping and extends the features of Simbiotics with live graph plotting and parameter sensitivity analysis.

Documentation

To learn how to run and configure Simbiotics, read the user manual. To learn how to develop and analyse models with Easybiotics, read this user guide. Check the project wiki for more information (usage tutorial, models gallery and case studies).

Download

You can download the Simbiotics source code (GNU GPLv3) and install the dependencies yourself or download the ready to use Simbiotics virtual machine image (with all dependencies pre-installed).

The source code is also available on BitBucket. Please report any issues you find there.

Project team

• Jonathan Naylor
• Harold Fellermann
• Natalio Krasnogor

Publications

If you use Simbiotics, please cite the following publication:

• DOI code BibTeX
  J. Naylor, H. Fellermann, Y. Ding, W.K. Mohammed, N.S. Jakubovics, J. Mukherjee, C.A. Biggs, P.C. Wright, N. Krasnogor
  Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations
  in ACS Synthetic Biology, 6(7):1194-1210, July 2017

  @ARTICLE{Naylor2017,
    title = {Simbiotics: A Multiscale Integrative Platform for 3D Modeling of Bacterial Populations},
    author = {Naylor, Jonathan and Fellermann, Harold and Ding, Yuchun and Mohammed, Waleed K. and Jakubovics, Nicholas S. and Mukherjee, Joy and Biggs, Catherine A. and Wright, Phillip C. and Krasnogor, Natalio},
    year = 2017,
    doi = {10.1021/acssynbio.6b00315},
    month = jul,
    journal = {ACS Synthetic Biology},
    volume = {6},
    number = {7},
    pages = {1194--1210}
  }