GITIRBio: A Semantic and Distributed Service Oriented- Architecture for Bioinformatics Pipeline

Abstract

Summary The need to process large quantities of data generated from genomic sequencing has resulted in a difficult task for life scientists who are not familiar with the use of command-line operations or developments in high performance computing and parallelization. This knowledge gap, along with unfamiliarity with necessary processes, can hinder the execution of data processing tasks. Furthermore, many of the commonly used bioinformatics tools for the scientific community are presented as isolated, unrelated entities that do not provide an integrated, guided, and assisted interaction with the scheduling facilities of computational resources or distribution, processing and mapping with runtime analysis. This paper presents the first approximation of a Web Services platform-based architecture (GITIRBio) that acts as a distributed front-end system for autonomous and assisted processing of parallel bioinformatics pipelines that has been validated using multiple sequences. Additionally, this platform allows integration with semantic repositories of genes for search annotations. GITIRBio is available at: http://c-head.ucaldas.edu.co:8080/gitirbio

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor

“…Individual studies can generate gigabytes and even petabytes of data [ 2 , 3 ]. Examples include -omics data [ 2 , 4 ], high-resolution imagery [ 5 ], lidar [ 6 ], and real-time monitoring data [ 3 ]. Additionally, simulation has emerged as a third branch of science to complement empirical and theoretical approaches [ 7 ].…”