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BacSim-T6SS

An agent-based model to simulate bacteria with type VI secretion system

Authors: Yuexia Luna Lin FlexLab, Ecole Polytechnique Federale de Lausanne, Switzerland

Chris H. Rycroft Department of Mathematics, University of Wisconsin-Madison

Software/library requirements:

  • GNUMake
  • GNU GCC compiler
  • GSL (GNU Scientific Library)
  • Perl (For image processing only)
  • Povray 3.7 (For image processing only)
  • FFMPEG (For making movies)

Get started:

  1. Download or git clone BacSim-T6SS repository.
  2. Modify the config.mk file to configure which compiler to use and basic compiler and linker flags. The default config.mk file provide Mac Ports installed GCC 9 on Macs, another sample config for Linux systems is provided in the configs/ folder.
  3. After these changes, type make in the command line in BacSim-T6SS/ directory, which will build an executable run_sim. This executable will use OpenMP to parallelize the computation if it is available.
  4. To run the executable, a simulation config file (must have file extension .cfg) for the simulation must be provided as the only command line argument.
  5. Sample simulation config files can be found in sim_configs/ directory. Examples include
  • si-movie-1.cfg : competition between wildtype ES401 and wildtype FQ-A002, where both lethal strains start from liquid culture T6SS activity level. The simulation uses periodic boundary condition to mimic the interior of a colony.
  • si-movie-2.cfg : competition between wildtype ES401 and wildtype FQ-A002, where both lethal strains start with fully activated T6SS. Boundary condition is the same as above.
  • si-movie-3.cfg : competition between a T6SS+ lethal strain and a nonlethal strain that does not fire any T6SS attacks, in a range expansion.

These examples produce the data files needed to render the corresponding supplementary movies in the manuscript listed below.

  1. If POV-Ray is installed and the necessary output files (f.%05d_nr%d) are available, the perl script pov-movie.pl can be used to render the output files. For example, if we want to render every frame in the directory my_sim.out/ and then link them into a movie, we can issue the command 
     perl pov-movie.pl -m my_sim.out
    where -m is a flag that tells the script to call ffmpeg and link the rendered pngs into a movie. In the pov_headers/ directory, we also provide some header files that define the colors, textures, and other rendering features for POV-Ray. For detailed usage of pov-movie.pl, see the help page by typing 
     perl pov-movie.pl -h

More complete documentation is under development. In the meantime, for any questions, feel free to contact the authors of this repository.

Acknowledgement

This work has been partially supported by the Applied Mathematics Program of the U.S. DOE Office of Science Advanced Scientific Computing Research under contract number DE-AC02-05CH11231, the Department of Energy Computational Science Graduate Fellowship, and the Harvard NSF-Simons Center Quantitative Biology Initiative student fellowship, supported by the National Science Foundation grant DMS-1764269.

References

Y.L.L, S.N.S., E.K., A.N.S, and C.H.R. "A subcellular biochemical model for T6SS dynamics reveals winning competitive strategies," in preparation.