NUFEB Documentation

NUFEB (Newcastle University Frontier in Engineering Biology) is an open source tool for 3D individual-based simulation of microbial communities. The tool is distributed under the terms of the GNU Public License (GPL).

NUFEB is built on top of the molecular dynamic simulator LAMMPS (version: stable_23Jun2022), and extended with features for microbial modelling. LAMMPS is an open-source code, distributed under the terms of the GPL. For more information about LAMMPS look at LAMMPS homepage.

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This site contains user and programmer documentation for the NUFEB use. If you find errors or omissions in the manual or have suggestions for useful information to add, please send an email to the developers.

NUFEB Development team:

Bowen Li, bowen.li2@newcastle.ac.uk

Denis Taniguchi: denis.taniguchi@newcastle.ac.uk

Joseph E. Weaver: joe.weaver@newcastle.ac.uk

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User Guide

• 1. Introduction
  • 1.1. What is NUFEB
  • 1.2. What is Individual-based Model
  • 1.3. NUFEB general features
  • 1.4. NUFEB model features
  • 1.5. Acknowledgments
  • 1.6. NUFEB development team
  • 1.7. Citing NUFEB
• 2. Install NUFEB on Linux & Mac
  • 2.1. Pre-compilation instructions
  • 2.2. Downloading NUFEB
  • 2.3. Compiling NUFEB
• 3. Install NUFEB on Windows
  • 3.1. Install Windows Subsystem for Linux
  • 3.2. Installing Linux distros from Microsoft Store
  • 3.3. Installing NUFEB
• 4. Run NUFEB
  • 4.1. Run NUFEB from terminal
  • 4.2. Run NUFEB on Code Ocean
• 5. Input Script
  • 5.1. Input script structure
  • 5.2. General settings
  • 5.3. Microbes, nutrients and simulation box
  • 5.4. IbM processes
  • 5.5. Computations and outputs
  • 5.6. Run
• 6. Commands
  • 6.1. Microbes and substrates
  • 6.2. Biological processes
  • 6.3. Physical processes
  • 6.4. Post-physical processes
  • 6.5. Chemical processes
  • 6.6. Reactor processes
  • 6.7. Computes
  • 6.8. Outputs
  • 6.9. Run
• 7. Optional packages

Tutorial

• 1. Workshop: modelling microbial dynamics in soil
  • 1.1. Run simulations on Code Ocean
  • 1.2. Run NUFEB on Code Ocean
• 2. Extend NUFEB with new growth model
  • 2.1. Define system
  • 2.2. Prepare input files
• 3. Managing Multiple Simulations with Snakemake
  • 3.1. Overview
  • 3.2. Why Snakemake
  • 3.3. Essential resources
  • 3.4. Setting up and running multiple simulations in Snakemake
  • 3.5. Implementation details
  • 3.6. Further reading
• 4. Editing NUFEB code
  • 4.1. Overview
  • 4.2. Printing a notice when a new microbe is formed
• 5. Adding Type VI Secretion System Interactions
  • 5.1. Overview
  • 5.2. Essential resources
  • 5.3. Modifying tutorial.nufeb

Cookbook

• 1. Stopping simulations at a consistent percent biomass
• 2. Creating a file to indicate the run completed successfully
• 3. Altering the dimensions of the simulation box
• 4. Saving simulation output to a CSV file
• 5. Computing species relative abundances

Command Reference

• Microbes and substrates
• Biological processes
• Physical processes
• Post-physical processes
• Chemical processes
• Reactor processes
• Computes
• Outputs
• Run

Indices and tables

• Index

• Search Page