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
    • fix nufeb/growth/anammox command
    • fix nufeb/growth/aob command
    • fix nufeb/growth/cyano command
    • fix nufeb/growth/ecoli command
    • fix nufeb/growth/energy command
    • fix nufeb/growth/eps command
    • fix nufeb/growth/het command
    • fix nufeb/growth/monod command
    • fix nufeb/growth/nob command
    • fix nufeb/growth/simple command
    • fix nufeb/division/coccus command
    • fix nufeb/division/bacillus command
    • fix nufeb/eps_secretion command
    • fix nufeb/death/diameter command
    • fix nufeb/T6SS/lysis command
    • fix nufeb/T6SS/contact command
  • Physical processes
  • Post-physical processes
  • Chemical processes
  • Reactor processes
  • Computes
  • Outputs
  • Run
NUFEB-manual
  • Biological processes
  • View page source

Biological processes

  • fix nufeb/growth/anammox command
  • fix nufeb/growth/aob command
  • fix nufeb/growth/cyano command
  • fix nufeb/growth/ecoli command
  • fix nufeb/growth/energy command
  • fix nufeb/growth/eps command
  • fix nufeb/growth/het command
  • fix nufeb/growth/monod command
  • fix nufeb/growth/nob command
  • fix nufeb/growth/simple command
  • fix nufeb/division/coccus command
  • fix nufeb/division/bacillus command
  • fix nufeb/eps_secretion command
  • fix nufeb/death/diameter command
  • fix nufeb/T6SS/lysis command
  • fix nufeb/T6SS/contact command
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