Title :
A soft IP core generating SoCs for the efficient stochastic simulation of large Biomolecular Networks using FPGAs
Author :
Hazapis, O.G. ; Logaras, E. ; Manolakos, Elias S.
Author_Institution :
Dept. of Inf. & Telecommun., Univ. of Athens, Athens, Greece
Abstract :
A soft IP core, expressed in parametric VHDL, has been developed and used to synthesize different multiprocessor Systems on Chip (SoCs) for the stochastic simulation of large-size biochemical reaction networks based on Gillespie´s First Reaction Method (FRM). The SoCs can be configured to have up to N=8 Processing Elements and simulate efficiently in hardware biomolecular networks with up to m=16K reactions. The FPGA implementations of the SoCs are communicating with a host PC via the serial and Ethernet ports for control and data transmission respectively. When mapped to a Virtex-5 Xilinx FPGA the FRM SoCs can deliver simulation performance (in Mega-Reactions/sec) that may exceed by up to two orders of magnitude the performance of well known software simulators running on fast PCs.
Keywords :
biomolecular electronics; data communication; field programmable gate arrays; local area networks; microprocessor chips; multiprocessing systems; stochastic processes; system-on-chip; Ethernet ports; FPGA implementations; FRM SoC; Gillespie´s first reaction method; Virtex-5 Xilinx FPGA; data transmission; hardware biomolecular networks; large-size biochemical reaction networks; multiprocessor systems on chip; parametric VHDL; processing elements; serial port; simulation performance; soft IP core; software simulators; stochastic simulation; Biological system modeling; Computer architecture; Field programmable gate arrays; Hardware; IP networks; Stochastic processes; System-on-a-chip;
Conference_Titel :
Electronics, Circuits and Systems (ICECS), 2012 19th IEEE International Conference on
Conference_Location :
Seville
Print_ISBN :
978-1-4673-1261-5
Electronic_ISBN :
978-1-4673-1259-2
DOI :
10.1109/ICECS.2012.6463795
