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Scooby
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The simulation of large systems of biochemical reactions is a key part of research into molecular
signaling and information processing in biological cells. However, it can be impractical because many
relevant reactions are modeled as stochastic, discrete event processes, and the complexity of the
computing task scales with the number of discrete events in a simulation. Traditionally, such
simulations are computed on general purpose CPUs, and sometimes in networks of such processors. We
show that an alternative algorithm to the conventional approaches based on the Gillespie algorithm
reveals a fine-grained parallel structure that is amenable to realization in FPGA hardware. A method
is shown for compiling biochemical reaction systems into corresponding Verilog descriptions of
simulators that employ this alternative algorithm. We describe a preliminary implementation of such a
compiled accelerator that demonstrates the performance of this approach, achieving an initial
performance that is 20 times faster than a competing general purpose CPU.
Keane, J.F., C. Bradley,
and C. Ebeling. A Compiled Accelerator for Biological Cell Signaling Simulations. in FPGA
2004 - Twelfth ACM International Symposium on Field-Programmable Gate Arrays. 2004. Monterey,
CA, USA: ACM.
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