NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities

Li, B.; Taniguchi, D.; Gedara, J. P.; Gogulancea, V.; Gonzalez-Cabaleiro, R.; Chen, J.; McGough, A. S.; Ofiteru, I. D.; Curtis, T. P.; Zuliani, P.

doi:10.1101/648204

bioRxiv · 10.1101/648204

NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities

Li, B.·Taniguchi, D.·Gedara, J. P.·Gogulancea, V.·Gonzalez-Cabaleiro, R.·Chen, J.·McGough, A. S.·Ofiteru, I. D.·Curtis, T. P.·Zuliani, P.

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Abstract

We present NUFEB, a flexible, efficient, and open source software for simulating the 3D dynamics of 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. This approach allows us to study population behaviours that emerge from the interaction between individuals and their environment. NUFEB is built on top of the classical molecular dynamics simulator LAMMPS, which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems. NUFEB is fully parallelised and allows for the simulation of large numbers of microbes (107 individuals and beyond). The parallelisation is based on a domain decomposition scheme that divides the domain into multiple sub-domains which are distributed to different processors. NUFEB also offers a collection of post-processing routines for the visualisation and analysis of simulation output. In this article, we give an overview of NUFEBs functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate.\n\nAuthor summaryIndividual-based Models (IbM) are one of the most promising frameworks to study microbial communities, as they can explicitly describe the behaviour of each cell. The development of a general-purpose IbM solver should focus on efficiency and flexibility due to the unique characteristics of microbial systems. However, available tools for these purposes present significant limitations. Most of them only facilitate serial computing for single simulation, or only focus on biological processes, but do not model mechanical and chemical processes in detail. In this work, we introduce the IbM solver NUFEB that addresses these shortcoming. The tool facilitates the modelling of much needed biological, chemical, physical and individual microbes in detail, and offers the flexibility of model extension and customisation. NUFEB is also fully parallelised and allows for the simulation of large complex microbial system. In this paper, we first give an overview of NUFEBs functionalities and implementation details. Then, we use NUFEB to model and simulate a biofilm system with fluid dynamics, and a large and complex biofilm system with multiple microbial functional groups and multiple nutrients.\n\nThis is a PLOS Computational Biology Software paper.

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Li, B., Taniguchi, D., Gedara, J. P., Gogulancea, V., Gonzalez-Cabaleiro, R., Chen, J., McGough, A. S., Ofiteru, I. D., Curtis, T. P., Zuliani, P.. 2019-05-24. NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities. https://doi.org/10.1101/648204

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