Cross-feeding

Introduction

This is a simulator for studying the cross-feeding mechanism based on kinetic Monte Carlo algorithm. The code written in C++ and it supports compiling in multiple platform.

Get Started

1. Compiling the simulator:

make <model-type>

There are four types of model types offered:

1. commensalism
2. syntrophy
3. mutualism
4. mutualism-tox

To access the debug mode add -d at the end of each type, as following:

1. commensalism-d
2. syntrophy-d
3. mutualism-d
4. mutualism-tox-d

Note that all compiled simulators are output to the subfolder bin/ with the same name as the <model-type>, access here

2. To start the simulation, use the following shell command:

./bin/<model-type> <parameter> <number-output-files> <output-directory>

Parameter description:

Parameter Name	Description
<model-type>	Type of the model used
<parameter>	Directory to parameter files
<number-output-files>	Number of output files, having the same time interval
<output-directory>	Directory stores all output files

3. To access the output files, go to the <output-directory> specified in previous step. Note that:
   1. All output files are three $n\times n$ matrices representing lattices of the colony and nutrient profiles.
      1. Colony are integers: 0 represents empty, 1 and 2 represent two types of species
      2. Nutrient are floating numbers representing the amount of nutrient produced in each lattice.
   2. Output files are in the format of .txt file, which can be easily accessed using common programming language.

Directory

• bin/
  • commensalism
  • mutualism
  • mutualism-tox
  • syntrophy
• include/
  • Array.h
  • ClockIt.h
  • Lattice.h
  • tools.h
• params/
  • default_param.txt
• src/
  • Lattice.cpp
  • main.cpp
  • tools.cpp
• LICENSE
• Makefile
• README.md

Citation

This is the code repository for article Emergence of sector and spiral patterns from a two-species mutualistic cross-feeding model (PONE-D-22-14372) for PLOS One.

Acknowledgement

The authors acknowledge the financial support from the National Science Foundation through grants DMR-1702321, MCB-2029480, and MCB-2029580. This work benefited from fruitful discussions with T. Hwa and B. Li. JJD is grateful for the hospitality of T. Hwa at UCSD during her sabbatical visit, where this project initiated.

License

Distributed under the MIT License. See LICENSE.txt for more information.