Advertisement

BactoSim – An Individual-Based Simulation Environment for Bacterial Conjugation

  • Antonio Prestes García
  • Alfonso Rodríguez-Patón
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9086)

Abstract

BactoSim is an agent-based platform for simulating the conjugation in spatially structured bacterial populations, which are the conditions typically found on naturally occurring colonies such as biofilms or in agar-based laboratory cultures. The model provides a set of key indicators which can be visualized in real time as the simulation evolves and saved as for further analysis.

Keywords

Basic Reproduction Number Conjugative Plasmid Mass Action Kinetic Bacterial Conjugation Single Bacterial Cell 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Beneš, D., Sosík, P., Rodríguez-Patón, A.: An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits. Artificial life, 1–14, January 2015. http://view.ncbi.nlm.nih.gov/pubmed/25622012
  2. 2.
    Norman, A., Hansen, L.H., Sørensen, S.J.: Conjugative plasmids: vessels of the communal gene pool. Philosophical transactions of the Royal Society of London. Series B, Biological Sciences 364(1527), 2275–2289 (2009). http://dx.doi.org/10.1098/rstb.2009.0037
  3. 3.
    North, M., Collier, N., Ozik, J., Tatara, E., Macal, C., Bragen, M., Sydelko, P.: Complex adaptive systems modeling with Repast Simphony. Complex Adaptive Systems Modeling 1(1), 1–26 (2013). http://dx.doi.org/10.1186/2194-3206-1-3
  4. 4.
    Seoane, J., Yankelevich, T., Dechesne, A., Merkey, B., Sternberg, C., Smets, B.F.: An individual-based approach to explain plasmid invasion in bacterial populations. FEMS Microbiology Ecology 75(1), 17–27 (2011). http://dx.doi.org/10.1111/j.1574-6941.2010.00994.x

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Antonio Prestes García
    • 1
  • Alfonso Rodríguez-Patón
    • 1
  1. 1.Departamento de Inteligencia ArtificialUniversidad Politécnica de MadridMadridSpain

Personalised recommendations