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. Further development was funded by the USF NSF Postdoctoral Research Fellowship in Biology Award #2007151.

Online user manual is avaiable at: https://nufeb.readthedocs.io/en/master/

Because NUFEB-2 is under active development and experimental, we would like you contact us if you use it. We'd enjoy hearing about how we could make it better AND we'd like to have a list of people to contact if major bugs are found. The best person to contact at this time would be Joseph E. Weaver: joe.weaver@newcastle.ac.uk

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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

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Developers:

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

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

Joseph E. Weaver: joe.weaver@newcastle.ac.uk