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Proceeding Paper

Parallelization of ARACNe, an Algorithm for the Reconstruction of Gene Regulatory Networks †

Grupo de Arquitectura de Computadores, CITIC, Universidade da Coruña, 15071 A Coruña, Spain
*
Author to whom correspondence should be addressed.
Presented at the 2nd XoveTIC Conference, A Coruña, Spain, 5–6 September 2019.
Proceedings 2019, 21(1), 25; https://doi.org/10.3390/proceedings2019021025
Published: 31 July 2019
(This article belongs to the Proceedings of The 2nd XoveTIC Conference (XoveTIC 2019))

Abstract

Gene regulatory networks are graphical representations of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression. There are different computational approaches for the reverse engineering of these networks. Most of them require all gene-gene evaluations using different mathematical methods such as Pearson/Spearman correlation, Mutual Information or topology patterns, among others. The Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) is one of the most effective and widely used tools to reconstruct gene regulatory networks. However, the high computational cost of ARACNe prevents its use over large biologic datasets. In this work, we present a hybrid MPI/OpenMP parallel implementation of ARACNe to accelerate its execution on multi-core clusters, obtaining a speedup of 430.46 using as input a dataset with 41,100 genes and 108 samples and 32 nodes (each of them with 24 cores).
Keywords: network reconstruction; ARACNe; High Performance Computing; MPI; OpenMP network reconstruction; ARACNe; High Performance Computing; MPI; OpenMP

Share and Cite

MDPI and ACS Style

Casal, U.; González-Domínguez, J.; Martín, M.J. Parallelization of ARACNe, an Algorithm for the Reconstruction of Gene Regulatory Networks. Proceedings 2019, 21, 25. https://doi.org/10.3390/proceedings2019021025

AMA Style

Casal U, González-Domínguez J, Martín MJ. Parallelization of ARACNe, an Algorithm for the Reconstruction of Gene Regulatory Networks. Proceedings. 2019; 21(1):25. https://doi.org/10.3390/proceedings2019021025

Chicago/Turabian Style

Casal, Uxía, Jorge González-Domínguez, and María J. Martín. 2019. "Parallelization of ARACNe, an Algorithm for the Reconstruction of Gene Regulatory Networks" Proceedings 21, no. 1: 25. https://doi.org/10.3390/proceedings2019021025

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