Automation of Metabolic P System Implementation in FPGA

Abstract

An original VHDL code generation tool that can be used to automate Metabolic P (MP) system implementation in hardware such as Field Programmable Gate Arrays (FPGA) is described. Unlike P systems, MP systems use a single membrane in their computations. Nevertheless there are many biological processes that have been successfully modeled by MP systems in a software. This is a first attempt to analyze MP system hardware implementations. Two different MP systems are investigated with the purpose of verifying the developed software: the model of Glucose-Insulin interactions in the intravenous glucose tolerance test (IVGTT) and the Non Photochemical Quenching process. The implemented systems’ calculation accuracy and hardware resource usage are examined. It is found that code generation tool works adequately however a final decision has to be done by developer because sometimes several implementation architecture alternatives have to be considered. As archetypical example serves IVGTT MP systems’ 21–23 bits FPGA implementations manifesting this in DSP, slice and 4 input LUT usage.