Genome-scale metabolic models. Modelling gene-protein-reaction associations on an FPGA

Academic Paper from the year 2019 in the subject Computer Science - Bioinformatics, , language: English, abstract: In this research a way to model GPRAs on an Altera Cyclone II FPGA was developed, using Quartus II programmable logic device design software and the VHDL hardware description language. The model consisting of 7 genes and 7 reactions was implemented using 7 combinational functions and 14 I/O pins.

Genome-scale metabolic models have proven to be incredibly useful. Allowing researchers to model cellular functionality based upon gene expression. However, as the number of genes and reactions increases, it can become computationally demanding. The first step in genome-scale metabolic modelling is to model the relationship between genes and reactions in the form of Gene-Protein-Reaction Associations (GPRA).

This model will be the first step towards creating a full genome scale metabolic model on FPGA devices which the author will be fully investigating in future studies.