1. Introduction
This section gives a brief overview of the NUFEB software and model, lists NUFEB key features, and acknowledges people who have contributed to NUFEB software and model developments.
1.1. What is NUFEB
NUFEB is an open-source individual based model tool for simulating the 3D dynamics of cell populations at the micro-scale. The tool is built on top of the molecular dynamic simulator LAMMPS, extended with features for biological system modelling. NUFEB offers the realistic explicit models of biological, chemical and physical processes, as well as individual cell in different shapes.
NUFEB takes full advantage of the LAMMPS parallel infrastructure, allowing for massive parallel simulations on both CPU- and GPU-based parallel computers. On the other hand, it can also be built and run on laptop or desktop machine.
1.2. What is Individual-based Model
Individual-based Model (IbM) is a computational model for simulating the actions and interactions of autonomous individuals, which, in our case, are the cells.
IbMs precisely capture how the heterogeneity of individual organisms and local interactions influence emergent behaviours, such as bacterial colony morphology.
In IbM, microbes are represented as rigid particles, each with their own set of biological and physical properties. These properties are affected by internal or external processes, resulting in cell growth, decay, motility, etc.
1.3. NUFEB general features
open-source distribution
runs on a single processor or in parallel
CPU parallelism support for all features (MPI, OpenMP)
GPU parallelism support for partial features (Kokkos)
runs from an input script
syntax for defining and using variables and formulas
syntax for looping over runs and breaking out of loops
run one or multiple simulations simultaneously (in parallel) from one script
output to VTK or HDF5 data format
output to PNG or JPEG image files
easy to extend with new features and functionality
build as library, invoke by other programme
1.4. NUFEB model features
spherical, rod, and ellipsoid cell representations
flexible definition of cell distributions
3d computational domain
continuous field for solute or gas distribution
biological processes (growth, division, plasmid replication, etc)
chemical processes (nutrient diffusion, pH, energy, etc)
DEM-based physical processes (repulsive force, adhesion, etc)
OpenFOAM integration for simulating fluid dynamics (CFD-DEM coupling)
1.5. Acknowledgments
NUFEB development has been funded by the following sources:
UK EPSRC EP/K039083/1 Frontiers in Engineering Biology project
UK EPSRC IAA (Impact Acceleration Accounts) award
1.6. NUFEB development team
NUFEB is developed at Newcastle University, UK.
1.7. Citing NUFEB
The following paper describes NUFEB (v1.0)’s functionalities and implementation details:
Li B, Taniguchi D, Gedara JP, Gogulancea V, Gonzalez-Cabaleiro R, et al. (2019) NUFEB: A massively parallel simulator for individual-based modelling of microbial communities. PLOS Computational Biology 15(12): e1007125. https://doi.org/10.1371/journal.pcbi.1007125