NUFEB is an open source tool for modelling and simulating microbial communities. The tool is based on the Individual-based Modelling (IbM) approach, where microbes are represented as discrete units and their behaviour changes over time due to a variety of processes.

NUFEB is built on top of the molecular dynamics simulator LAMMPS (as a LAMMPS' user package), extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems.

NUFEB is a freely-available open-source code, distributed under the terms of the GNU Public License.

NUFEB development has been funded by the UK’s EPSRC EP/K039083/1 Newcastle University Frontiers in Engineering Biology (NUFEB) project.

You can find tutorial and example videos in the NUFEB Wiki page.

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         visualisation routine 
src                     source files 
thirdparty              thirdparty tools

Get NUFEB source code and submodules for its thirdparty libraries:

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

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

Build NUFEB essential features without vtk or hdf5:

./install.sh

Build NUFEB with vtk:

cd thirdparty
./install-vtk.sh
cd ..
./install.sh --enable-vtk

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

cd examples/biofilm-monod
mpirun -np 4 ../../lammps/src/./lmp_mpi -in Inputscript.lammps

Developers:

Bowen Li: [email protected]

Denis Taniguchi: [email protected]