NUFEB: A massively parallel simulator for individual-based modelling of microbial communities.
We present NUFEB (Newcastle University Frontiers in Engineering Biology), 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...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-12-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007125&type=printable |
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| author | Bowen Li Denis Taniguchi Jayathilake Pahala Gedara Valentina Gogulancea Rebeca Gonzalez-Cabaleiro Jinju Chen Andrew Stephen McGough Irina Dana Ofiteru Thomas P Curtis Paolo Zuliani |
| author_facet | Bowen Li Denis Taniguchi Jayathilake Pahala Gedara Valentina Gogulancea Rebeca Gonzalez-Cabaleiro Jinju Chen Andrew Stephen McGough Irina Dana Ofiteru Thomas P Curtis Paolo Zuliani |
| author_sort | Bowen Li |
| collection | DOAJ |
| description | We present NUFEB (Newcastle University Frontiers in Engineering Biology), 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 (Large-scale Atomic/Molecular Massively Parallel Simulator), which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems, with particular emphasis on biofilms. 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 NUFEB's functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate. |
| format | Article |
| id | doaj-art-56d5cf548f5e4abb813363c97f5003da |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2019-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-56d5cf548f5e4abb813363c97f5003da2025-08-20T02:17:05ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582019-12-011512e100712510.1371/journal.pcbi.1007125NUFEB: A massively parallel simulator for individual-based modelling of microbial communities.Bowen LiDenis TaniguchiJayathilake Pahala GedaraValentina GogulanceaRebeca Gonzalez-CabaleiroJinju ChenAndrew Stephen McGoughIrina Dana OfiteruThomas P CurtisPaolo ZulianiWe present NUFEB (Newcastle University Frontiers in Engineering Biology), 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 (Large-scale Atomic/Molecular Massively Parallel Simulator), which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems, with particular emphasis on biofilms. 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 NUFEB's functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007125&type=printable |
| spellingShingle | Bowen Li Denis Taniguchi Jayathilake Pahala Gedara Valentina Gogulancea Rebeca Gonzalez-Cabaleiro Jinju Chen Andrew Stephen McGough Irina Dana Ofiteru Thomas P Curtis Paolo Zuliani NUFEB: A massively parallel simulator for individual-based modelling of microbial communities. PLoS Computational Biology |
| title | NUFEB: A massively parallel simulator for individual-based modelling of microbial communities. |
| title_full | NUFEB: A massively parallel simulator for individual-based modelling of microbial communities. |
| title_fullStr | NUFEB: A massively parallel simulator for individual-based modelling of microbial communities. |
| title_full_unstemmed | NUFEB: A massively parallel simulator for individual-based modelling of microbial communities. |
| title_short | NUFEB: A massively parallel simulator for individual-based modelling of microbial communities. |
| title_sort | nufeb a massively parallel simulator for individual based modelling of microbial communities |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007125&type=printable |
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