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dc.contributor.authorKarim, Md. Rezaul
dc.contributor.authorMichel, Audrey
dc.contributor.authorZappa, Achille
dc.contributor.authorBaranov, Pavel
dc.contributor.authorSahay, Ratnesh
dc.contributor.authorRebholz-Schuhmann, Dietrich
dc.identifier.citationKarim, Md Rezaul, Michel, Audrey, Zappa, Achille, Baranov, Pavel, Sahay, Ratnesh, & Rebholz-Schuhmann, Dietrich. (2017). Improving data workflow systems with cloud services and use of open data for bioinformatics research. Briefings in Bioinformatics, bbx039-bbx039. doi: 10.1093/bib/bbx039en_IE
dc.description.abstractData workflow systems (DWFSs) enable bioinformatics researchers to combine components for data access and data analytics, and to share the final data analytics approach with their collaborators. Increasingly, such systems have to cope with large-scale data, such as full genomes (about 200 GB each), public fact repositories (about 100 TB of data) and 3D imaging data at even larger scales. As moving the data becomes cumbersome, the DWFS needs to embed its processes into a cloud infrastructure, where the data are already hosted. As the standardized public data play an increasingly important role, the DWFS needs to comply with Semantic Web technologies. This advancement to DWFS would reduce overhead costs and accelerate the progress in bioinformatics research based on large-scale data and public resources, as researchers would require less specialized IT knowledge for the implementation. Furthermore, the high data growth rates in bioinformatics research drive the demand for parallel and distributed computing, which then imposes a need for scalability and high-throughput capabilities onto the DWFS. As a result, requirements for data sharing and access to public knowledge bases suggest that compliance of the DWFS with Semantic Web standards is necessary. In this article, we will analyze the existing DWFS with regard to their capabilities toward public open data use as well as large-scale computational and human interface requirements. We untangle the parameters for selecting a preferable solution for bioinformatics research with particular consideration to using cloud services and Semantic Web technologies. Our analysis leads to research guidelines and recommendations toward the development of future DWFS for the bioinformatics research community.en_IE
dc.description.sponsorshipThe Science Foundation Ireland (grant number SFI/12/RC/2289).en_IE
dc.publisherOxford University Pressen_IE
dc.relation.ispartofBriefings in Bioinformaticsen
dc.rightsAttribution-NonCommercial-NoDerivs 3.0 Ireland
dc.subjectData workflow systemen_IE
dc.subjectSemantic Weben_IE
dc.subjectLinked dataen_IE
dc.subjectCloud computingen_IE
dc.subjectGenome sequencingen_IE
dc.subjectDrug discoveryen_IE
dc.titleImproving data workflow systems with cloud services and use of open data for bioinformatics researchen_IE
dc.contributor.funderScience Foundation Irelanden_IE
dc.local.contactRatnesh Nandan Sahay, Deri, Dangan Business Park, Nui Galway. 5253 Email:
dcterms.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2289/IE/INSIGHT - Irelands Big Data and Analytics Research Centre/

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