Parallel computing platform for the agent-based modeling of multicellular biological systems

Authors:
Toh Da-Jun;Francis Tang;Travis Lee;Deepak Sarda;Arun Krishnan;Andrew Goryachev
Affiliations:
Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore
Venue:
PDCAT'04 Proceedings of the 5th international conference on Parallel and Distributed Computing: applications and Technologies
Year:
2004

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Abstract

Agent-based simulation of large multicellular biological systems has become a viable option owing to affordable parallel computers, such as Beowulf-style clusters. We describe a scalable modular software platform that (i) provides for an easy integration of different solvers computing internal dynamics of the cells, and (ii) dynamically adapts to the changing loads on the cluster nodes using a load balancing algorithm. Simulations of systems of about 100,000 bacterial cells have been shown to be feasible using the platform.