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Biofilms: United They Stand, Divided They Colonize

By Angela B. Shiflet, George W. Shiflet and Shay M. Ellison*
Wofford College, Spartanburg, South Carolina
*now at Florida State University, Tallahassee, Florida

This page provides download links for a set of curricular materials designed to teach parallel computational modeling to undergraduate or graduate students in science and other STEM disciplines. The module begins with the construction of a cellular automaton model of microbial biofilms using Mathematica. This model is then re-implemented with C and parallelized using MPI. The module consists of the documents described below. The documents can be downloaded individually, or as a zip archive containing all of the documents:

Resources:

Biofilms Module.doc : MS Word file describing:

  • Biofilms
  • Cellular automata modeling
  • Algorithms and model implementation
  • Simulation results
  • Assessment rubrics
  • Project ideas
  • Examples & solutions
  • References

Biofilm.nb : Implementation of the Biofilms sequential model as a Mathematica notebook file.

Biofilm_Description.pdf : A pdf version of Biofilm model in Mathematica that can be easily printed and displayed

MPI_Biofilm_Description.doc : MS Word file detailing the steps for creating a parallel version of the biofilms project using MPI and C to run on any MPI enabled architecture with a function library for parallel random number generation called SPRNG

BiofilmParallelDual.c : Source code in C with MPI for the parallel implementation of the Biofilm model for systems with two processors

BiofilmParallelMulti.c : Source code in C with MPI for the parallel implementation of the Biofilms model for systems with multiple processors

Biofilms Module Archive.zip : Zip archive containing all of the materials for the Biofilms Module