BacGrid: Simulations of Bacteria using the GRID
Description
Bacterial biofilms provide systems of the complexity needed to exemplify
many of the generic features of multi-cellular behaviour, without such
complexity at once becoming overwhelming. They are in addition of
enormous environmental, industrial and medical importance. Many
processes in biofilms operate at the macroscopic scale and are thus
susceptible continuum modelling approaches. It is essential, however,
that models incorporate in an appropriate way information about the
micro-scale behaviour and their results must in turn be coupled back
into the rules adopted in the cell-scale modelling, motivating the use
of agent-based modelling. The simulation of such complex systems
typically requires huge computing resources. The Grid provides an
unrivalled technology for large scale distributed simulation and is
exceptionally well suited to addressing the challenges raised by
integrative-biology. In this paper we present BacGrid, a system for
performing distributed simulation of bacteria using the High
Level Architecture (HLA) and the Grid. We present the bacterial model
and show results from initial experiments investigating the role of
quorum sensing molecule (QSM) in the development of the bacterial
colony. We go on to sketch out the design for the distribution of
bacterial simulation components across the grid and indicate how this
technology can be used to create large scale simulations. We conclude
with a discussion of the current status of the system and our plans for
future work and experiments.
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