ReCSiP: An FPGA‐based general‐purpose biochemical simulator
Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko F. Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, Hideharu Amano · Electronics and Communications in Japan (Part II Electronics) · 2007
Abstract Mathematical modeling and simulation of cellular systems are essential to modern biological researches. However, simulating with software‐based simulators on general‐purpose microprocessors cannot provide enough throughput. ReCSiP is an FPGA‐based solution for biochemical simulation and parameter scanning. This paper describes its design and hardware implementation. With Xilinx's XC2VP70‐5, this method achieved 50‐ to 80‐fold speed‐up compared to Intel's Pentium4 processor. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 90(7): 1–10, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecjb.20370