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
dump hdf5 command
dump image command
dump modify command
dump movie command
dump vtk/grid command
dump vtk command
Run
NUFEB-manual
Outputs
dump vtk command
View page source
dump vtk command