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HIV modelling - parallel implementation strategies

Perrin, Dimitri and Ruskin, Heather J. and Crane, Martin (2006) HIV modelling - parallel implementation strategies. In: Third International Conference on Cluster and Grip Computing Systems, 24-26 November 2006, Venice, Italy.

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Abstract

We report on the development of a model to understand why the range of experience with respect to HIV infection is so diverse, especially with respect to the latency period. To investigate this, an agent-based approach is used to extract highlevel behaviour which cannot be described analytically from the set of interaction rules at the cellular level. A network of independent matrices mimics the chain of lymph nodes. Dealing with massively multi-agent systems requires major computational effort. However, parallelisation methods are a natural consequence and advantage of the multi-agent approach and, using the MPI library, are here implemented, tested and optimized. Our current focus is on the various implementations of the data transfer across the network. Three communications strategies are proposed and tested, showing that the most efficient approach is communication based on the natural lymph-network connectivity.

Item Type:Conference or Workshop Item (Paper)
Event Type:Conference
Refereed:Yes
Uncontrolled Keywords:HIV; immune modelling; MPI; parallelisation;
Subjects:Computer Science > Computational complexity
Mathematics > Mathematical models
Medical Sciences > Diseases
Biological Sciences > Immunology
Biological Sciences > Virology
DCU Faculties and Centres:DCU Faculties and Schools > Faculty of Engineering and Computing > School of Computing
Official URL:http://www.enformatika.org/cgcs06/
Use License:This item is licensed under a Creative Commons Attribution-NonCommercial-Share Alike 3.0 License. View License
ID Code:9
Deposited On:31 Oct 2006 by DORAS Administrator. Last Modified 29 Jan 2009 16:24

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