NUFEB-2

KO | EN

gitlite — search

#python #react #llm #golang #android #linux #nodejs #java #windows #cli #vue #security #ios #open-source

(★ 9)

NUFEB development repository

NUFEB-2 Latest Version Download

Download Latest Version (.zip)

// repository documentation

Was this content helpful?

★ 0 (0 ratings)

<h1 align="center">NUFEB: Agent-based Simulator for Modelling Cell Populations</h1>

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](https://lammps.sandia.gov), and extended with features for microbial modelling. 
For more details about NUFEB and its agent-based model, please refer to our [software paper](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007125).

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/

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 NUFEB distribution includes the following files and directories:
<pre>
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
</pre>

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:
<pre>
sudo apt update
sudo apt-get install cmake git-core g++ openmpi-bin openmpi-common libopenmpi-dev libpng-dev ffmpeg
</pre>

On CentOS:
<pre>
sudo yum update
sudo yum install cmake git gcc-c++ openmpi openmpi-devel libpng-dev ffmpeg
</pre>

On Windows:

Follow the [tutorial](https://nufeb.readthedocs.io/en/master/install_win.html) to use NUFEB on Windows (via WSL).

### Getting source
Get NUFEB source code:
<pre>
git clone https://github.com/nufeb/NUFEB-2
</pre>

### Building
<pre>
./install.sh
</pre>

### Running
Run an example simulation (heterotrophic biofilm growth):
<pre>
cd examples/biofilm-heterotroph
mpirun -np 4 ../../nufeb_mpi -in Inputscript.nufeb
</pre>

---------------------------------------------------------------------------
### Current Developers:

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

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

---------------------------------------------------------------------------
### Further development was funded by:

EPSRC Portabolomics (Grant EP/N031962/1)

EPSRC Impact Acceleration Account (IAA) Award

USF NSF Postdoctoral Research Fellowship in Biology (Award #2007151)

Rosetrees Trust AI-PSORT (Award CF-2021-2\111)

NUFEB-2

NUFEB-2 Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

NUFEB-2

NUFEB-2 Latest Version Download

Today's picks

Was this content helpful?

Recent Feedback

Download README