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
compute nufeb/ave_conc command
compute nufeb/ave_length command
compute nufeb/density command
compute nufeb/volume command
Outputs
Run
NUFEB-manual
Computes
compute nufeb/density command
View page source
compute nufeb/density command