Abstract:
The study of biological regulatory networks constitutes an important area in systems
biology. Several modeling approaches have been introduced to describe the behavior of these
networks. Qualitative modeling approach presented by Ren´e Thomas has been widely used
to discover dynamic properties of biological networks. A number of software tools have
been developed to study and analyze biological networks using this formalism . However
due to large parameter space, huge amount of computational resources are required to
study large networks.
In last few years, reconfigurable hardware devices such as field programmable gate
arrays (FPGA) have demonstrated huge computational power. Due to their high compu tational capability and low power consumption, FPGA offer attractive platform to develop
computational applications.
In this work, we implement Ren´e Thomas modeling approach on FPGA. We used verilog
language for FPGA programming. A C++ application programming interface (API) is
developed that reads input file to extract biological network and generate verilog code on
runtime time for FPGA. The important qualitative properties of biological networks such
as stable states and oscillations (cycles) are computed on FPGA. The experiments were
simulated for Virtex-6 FPGA ML605 using Xilinx ISE Design Suite version 13.1. This
design checks sysntax of program,simulate verilog code and generate top level module and
circuit diagrams. The experimental results, when compared to desktop computers, show
huge performance gain and dramatic reduction in processing time.
