Kabiri Chimeh, M. orcid.org/0000-0002-2561-7926, Heywood, P., Pennisi, M. et al. (2 more authors) (2019) Parallelisation strategies for agent based simulation of immune systems. BMC Bioinformatics, 20. 579.
Abstract
Background
In recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological domain due to high demand for a large scale analysis tools for the collection and interpretation of information to solve biological problems. Simulating massive multi-agent systems (i.e. simulations containing a large number of agents/entities) requires major computational effort which is only achievable through the use of parallel computing approaches.
Results
This paper explores different approaches to parallelising the key component of biological and immune system models within an ABM model: pairwise interactions. The focus of this paper is on the performance and algorithmic design choices of cell interactions in continuous and discrete space where agents/entities are competing to interact with one another within a parallel environment.
Conclusions
Our performance results demonstrate the applicability of these methods to a broader class of biological systems exhibiting typical cell to cell interactions. The advantage and disadvantage of each implementation is discussed showing each can be used as the basis for developing complete immune system models on parallel hardware.
Metadata
Item Type: | Article |
---|---|
Authors/Creators: |
|
Copyright, Publisher and Additional Information: | © 2019 The Authors. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
Keywords: | Agent based modeling; GPGPU; High-performance computing; Cellular modelling; Computational modelling; Parallel simulation; FLAME GPU |
Dates: |
|
Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Computer Science (Sheffield) |
Funding Information: | Funder Grant number ENGINEERING AND PHYSICAL SCIENCE RESEARCH COUNCIL (EPSRC) EP/N018869/1 EUROPEAN COMMISSION - HORIZON 2020 777123 |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 20 Jan 2020 10:12 |
Last Modified: | 20 Jan 2020 10:17 |
Status: | Published |
Publisher: | Springer Science and Business Media LLC |
Refereed: | Yes |
Identification Number: | 10.1186/s12859-019-3181-y |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:155217 |
Download
Filename: Parallelisation strategies for agent based simulation of immune systems.pdf
Licence: CC-BY 4.0