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
fix nufeb/diffusion_reaction command
fix nufeb/gas_liquid command
fix nufeb/reactor/gas_balance command
fix nufeb/reactor/solute_balance command
Reactor processes
Computes
Outputs
Run
NUFEB-manual
Chemical processes
fix nufeb/gas_liquid command
View page source
fix nufeb/gas_liquid command