NUFEB: Agent-based Simulator for Modelling Cell Populations
This is the NUFEB repository.
NUFEB (Newcastle University Frontier in Engineering Biology) is an open source tool for 3D agent-based simulation of microbial systems. The tool is built on top of the molecular dynamic simulator LAMMPS, and extended with features for microbial modelling. For more details about NUFEB and its agent-based model, please refer to our software 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.
Online user manual is avaiable at: https://nufeb.readthedocs.io/en/master/
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 docs source of user manual and other documentations examples test problems and cases used in publications lib libraries NUFEB can be linked with lammps_stable_23Jun2022 LAMMPS source code src source files thirdparty thirdparty tools
NUFEB requires cmake, git, gcc/g++, openmpi, png-dev and ffmpeg for a successful build. You can run the following commands to install the packages,
On Ubuntu:
sudo apt update sudo apt-get install cmake git-core g++ openmpi-bin openmpi-common libopenmpi-dev libpng-dev ffmpeg
On CentOS:
sudo yum update sudo yum install cmake git gcc-c++ openmpi openmpi-devel libpng-dev ffmpeg
On Windows:
Follow the tutorial to use NUFEB on Windows (via WSL).
Getting source
Get NUFEB source code:
git clone https://github.com/nufeb/NUFEB-2
Building
./install.sh
Running
Run an example simulation (heterotrophic biofilm growth):
cd examples/biofilm-heterotroph mpirun -np 4 ../../nufeb_mpi -in Inputscript.nufeb
Developers:
Bowen Li: bowen.li2@newcastle.ac.uk
Denis Taniguchi: denis.taniguchi@newcastle.ac.uk
Joseph E. Weaver: joe.weaver@newcastle.ac.uk