NUFEB (Newcastle University Frontier in Engineering Biology) is an open source tool for 3D individual-based simulation of microbial communities. The tool is built on top of the molecular dynamic simulator LAMMPS, and extended with features for microbial modelling. For more details about NUFEB software and model look at our paper.

NUFEB is distributed under the terms of the GNU Public License. The development has been funded by the UK’s EPSRC EP/K039083/1 Frontiers in Engineering Biology project.

Installation guide, tutorial, example videos, and more details can be found in NUFEB Wiki page and User Manual

The NUFEB distribution includes the following files and directories:

README                  this file 
LICENSE                 the GNU General Public License (GPL)
install.sh              script for building NUFEB 
uninstall.sh            script for uninstalling NUFEB 
doc                     user manual and other documentation 
examples                test problems and cases used in publications 
lib                     libraries NUFEB can be linked with 
lammps                  LAMMPS source code
post-processing         Povray visualisation routine 
src                     source files 
thirdparty              thirdparty tools

Getting source

Get NUFEB source code and submodules for its thirdparty libraries:

git clone https://github.com/nufeb/NUFEB --recursive

Building

NUFEB requires gcc/g++ and openmpi for a successful build.

Build NUFEB:

./install.sh

Running

Run a case in /examples after building NUFEB, for example:

cd examples/simple-growth
mpirun -np 4 lmp_mpi -in Inputscript.lammps

Developers:

Bowen Li: bowen.li2@newcastle.ac.uk

Denis Taniguchi: denis.taniguchi@newcastle.ac.uk