Biology Portal

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:

• Biofilms Module.doc contains the bulk of the content for the module. It provides sections describing:
  
  
  • Scientific background on biofilms
  • Cellular automata modeling and it's application to the modeling of biofilms
  • Algorithmic details and implementation of the computational approach
  • Simulation results
  • Rubrics for assessment of student work
  • Ideas for student projects
  • Solutions to example problems
  • References.
• Biofilm.nb is the implementation of the model as a Mathematica notebook file. A pdf version of this file that can be easily printed and displayed is also provided Biofilm.nb.pdf.
• MPI Biofilm Walkthrough.doc details 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.
• BiofilmParallel2.c is the parallel implementation of the model for systems with two processors.
• BiofilmParallelMulti.c is the parallel implementation of the model for systems with multiple processors.
• Biofilms_Module.zip is a zip archive containing all of the files listed above.