NUFEB-manual
0.0.1

User Guide

  • 1. Introduction
  • 2. Install NUFEB on Linux & Mac
  • 3. Install NUFEB on Windows
  • 4. Run NUFEB
  • 5. Input Script
  • 6. Commands
  • 7. Optional packages

Tutorial

  • 1. Workshop: modelling microbial dynamics in soil
  • 2. Extend NUFEB with new growth model
  • 3. Managing Multiple Simulations with Snakemake
  • 4. Editing NUFEB code
  • 5. Adding Type VI Secretion System Interactions

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
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