A system architecture for parallel analysis of flux-balanced metabolic pathways

TL;DR

This paper presents a GPU-based system architecture that models metabolic networks using an AND/OR graph, enabling efficient parallel analysis of flux-balanced pathways in metabolic pathways.

Contribution

It introduces a novel parallel architecture leveraging GPU and CUDA to analyze metabolic networks modeled as AND/OR graphs, enhancing computational efficiency.

Findings

Successfully applied to small and large networks

Achieved efficient parallel pathway analysis

Demonstrated scalability and effectiveness

Abstract

In this paper, a system architecture is proposed that approximately models the functionality of metabolic networks. The AND/OR graph model is used to represent the metabolic network and each processing element in the system emulates the functionality of a metabolite. The system is implemented on a graphics processing unit (GPU) as the hardware platform using CUDA environment. The proposed architecture takes advantage of the inherent parallelism in the network structure in terms of both pathway and metabolite traversal. The function of each element is defined such that it can find flux-balanced pathways. Pathways in both small and large metabolic networks are applied to the proposed architecture and the results are discussed.