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Bioinformatics Workflows With NoSQL Database in Cloud Computing.
Wercelens, Polyane; da Silva, Waldeyr; Hondo, Fernanda; Castro, Klayton; Walter, Maria Emília; Araújo, Aletéia; Lifschitz, Sergio; Holanda, Maristela.
Afiliação
  • Wercelens P; Department of Computer Science, University of Brasília, Brasília, Brazil.
  • da Silva W; Department of Computer Science, University of Brasília, Brasília, Brazil.
  • Hondo F; NEPBIO (Group of Biological Studies and Research on Cerrado), Federal Institute of Goiás (IFG), Formosa, Goiás, Brazil.
  • Castro K; Department of Computer Science, University of Brasília, Brasília, Brazil.
  • Walter ME; Department of Computer Science, University of Brasília, Brasília, Brazil.
  • Araújo A; Department of Computer Science, University of Brasília, Brasília, Brazil.
  • Lifschitz S; Department of Computer Science, University of Brasília, Brasília, Brazil.
  • Holanda M; Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil.
Evol Bioinform Online ; 15: 1176934319889974, 2019.
Article em En | MEDLINE | ID: mdl-31839702
Scientific workflows can be understood as arrangements of managed activities executed by different processing entities. It is a regular Bioinformatics approach applying workflows to solve problems in Molecular Biology, notably those related to sequence analyses. Due to the nature of the raw data and the in silico environment of Molecular Biology experiments, apart from the research subject, 2 practical and closely related problems have been studied: reproducibility and computational environment. When aiming to enhance the reproducibility of Bioinformatics experiments, various aspects should be considered. The reproducibility requirements comprise the data provenance, which enables the acquisition of knowledge about the trajectory of data over a defined workflow, the settings of the programs, and the entire computational environment. Cloud computing is a booming alternative that can provide this computational environment, hiding technical details, and delivering a more affordable, accessible, and configurable on-demand environment for researchers. Considering this specific scenario, we proposed a solution to improve the reproducibility of Bioinformatics workflows in a cloud computing environment using both Infrastructure as a Service (IaaS) and Not only SQL (NoSQL) database systems. To meet the goal, we have built 3 typical Bioinformatics workflows and ran them on 1 private and 2 public clouds, using different types of NoSQL database systems to persist the provenance data according to the Provenance Data Model (PROV-DM). We present here the results and a guide for the deployment of a cloud environment for Bioinformatics exploring the characteristics of various NoSQL database systems to persist provenance data.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Prognostic_studies Idioma: En Revista: Evol Bioinform Online Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Brasil País de publicação: Estados Unidos
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Prognostic_studies Idioma: En Revista: Evol Bioinform Online Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Brasil País de publicação: Estados Unidos