2015
DOI: 10.1186/s13742-015-0092-3
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Enhanced reproducibility of SADI web service workflows with Galaxy and Docker

Abstract: BackgroundSemantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services.FindingsThis article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to compl… Show more

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Cited by 14 publications
(10 citation statements)
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“…The advantage of exposing Bio2RDF as a set of SADI services is that the data in Bio2RDF becomes discoverable -software does not need to know, a priori, what data/relations exist in which Bio2RDF endpoint. Moreover, when exposed as SADI Services, Bio2RDF data can more easily be integrated into workflows using popular workflow editors such as Taverna 105 or as demonstrated by our use of these services within Galaxy workflows 106 .…”
Section: Bio2rdf2sadimentioning
confidence: 99%
“…The advantage of exposing Bio2RDF as a set of SADI services is that the data in Bio2RDF becomes discoverable -software does not need to know, a priori, what data/relations exist in which Bio2RDF endpoint. Moreover, when exposed as SADI Services, Bio2RDF data can more easily be integrated into workflows using popular workflow editors such as Taverna 105 or as demonstrated by our use of these services within Galaxy workflows 106 .…”
Section: Bio2rdf2sadimentioning
confidence: 99%
“…Docker provides a standard way to supply ready-to-use applications, and it's beginning to be a common way to share works [ 15 22 ]. In Aranguren and Wilkinson [ 23 ], the authors make the assumption that the reproducibility could be implemented at 2 levels: (1) at the Docker container level: the encapsulation of a tool with all its dependencies would ensure the sustainability, traceability, and reproducibility of the tool; and (2) at the workflow level: the reproducibility is ensured by Galaxy workflow definition. They developed a containerized Galaxy Docker platform in the context of the OpenLifeData2SADI research project.…”
Section: Introductionmentioning
confidence: 99%
“…Thus, Dockers technology is very suitable for the application in the field of bioinformatics, because of its advantages and characteristics that allow applications to run in an isolated, self-contained package that can be efficiently distributed and executed in a portable manner across a wide range of computing platforms. ( Belmann et al, 2015;Hosny et al, 2016;Aranguren and Wilkinson, 2015), At present, there are many bioinformatics tools based on docker are developed and published, such as perl and bioperl (Martini, 2016), python and biopython (Moghedrin et al, 2016), R and Bioconductor (Eddelbuettel et al, 2016), contribute their Official Docker image; famous Galaxy also contribute docker galaxy (Björn, 2016). It's reasonable to predict that docker will become more and more extensive in the field of bioinformatics.…”
Section: Introductionmentioning
confidence: 99%