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Modelling Gene-Protein-Reaction Associations on an FPGA

Coggins, M.

2019-06-03 bioinformatics
10.1101/658195 bioRxiv
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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). In this research we have developed a way to model GPRAs on an Altera Cyclone II FPGA 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. This model will be the first step towards creating a full genome scale metabolic model on FPGA devices which we will be fully investigating in future studies.

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