Abstract
Abstract An original Very High Speed Integrated Circuit Hardware Description Language (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 software. This is the 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 the developer because sometimes several implementation architecture alternatives have to be considered. As an archetypical example serves the IVGTT MP systems’ 21–23 bits FPGA implementation manifesting this in the Digital Signal Processor (DSP), slice, and 4-input LUT usage.
Highlights
Metabolic P (MP) systems evolved from and are based on membrane computing or P systems [1]
The MP system VHDL code generation tool written in Python interpreted programming language was developed to convert MP systems described by a text file in JavaScript Object Notation (JSON) format to VHDL architecture
MP systems, described in Sections III.B and III.C, were implemented in Field Programmable Gate Arrays (FPGA) using the VHDL code generated by the developed MP system VHDL code generation tool
Summary
Metabolic P (MP) systems evolved from and are based on membrane computing or P systems [1]. Any substances defined in a MP system are moved through this membrane or transform from one to another at a certain rate These systems are inspired by a biological process known as metabolism that is crucial for the survival of living organisms. It is a simulation tool developed for MP system modeling that allows describing a system by means of graphs and simulating the system dynamics based on metabolic algorithm. An improved version of the software called MetaPlab was introduced in [12] It features a new plug-in based architecture which makes the software more versatile and able to perform multiple tasks. Another implementation of MP systems is an open-source MpTheory Java Library.
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