A Reconfigurable Stochastic Model Simulator for Analysis of Parallel Systems
FCCM '00 Proceedings of the 2000 IEEE Symposium on Field-Programmable Custom Computing Machines
A parallel architecture for non-deterministic discrete event simulation
A parallel architecture for non-deterministic discrete event simulation
Optimized Generation of Data-Path from C Codes for FPGAs
Proceedings of the conference on Design, Automation and Test in Europe - Volume 1
Proceedings of the 41st annual Design Automation Conference
Low-power warp processor for power efficient high-performance embedded systems
Proceedings of the conference on Design, automation and test in Europe
Journal of VLSI Signal Processing Systems
Efficient hardware code generation for FPGAs
ACM Transactions on Architecture and Code Optimization (TACO)
High-performance computing with desktop workstations
MATH'06 Proceedings of the 10th WSEAS International Conference on APPLIED MATHEMATICS
Non-intrusive dynamic application profiler for detailed loop execution characterization
CASES '08 Proceedings of the 2008 international conference on Compilers, architectures and synthesis for embedded systems
CODES+ISSS '08 Proceedings of the 6th IEEE/ACM/IFIP international conference on Hardware/Software codesign and system synthesis
Scalability and parallel execution of warp processing: dynamic hardware/software partitioning
International Journal of Parallel Programming
ACM Transactions on Design Automation of Electronic Systems (TODAES)
Efficient hardware-based nonintrusive dynamic application profiling
ACM Transactions on Embedded Computing Systems (TECS)
Emulation of biological networks in reconfigurable hardware
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Proceedings of the great lakes symposium on VLSI
ACM Transactions on Embedded Computing Systems (TECS)
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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.