Enhanced reproducibility of SADI web service workflows with Galaxy and Docker

GigaScience

Mark D. Wilkinson¹  Mikel Egaña Aranguren² 

[1] Biological Informatics, Centre for Plant Biotechnology and Genomics (CBGP), Technical University of Madrid (UPM), Campus of Montegancedo, Pozuelo de Alarcón 28223, Spain;Eurohelp Consulting, Maximo Aguirre 18, Bilbo, 48011, Spain

关键词: Reproducibility;    Docker;    Galaxy;    Workflow;    Web service;    SADI;    RDF;    Semantic Web;   

Others  :  1234665
DOI  :  10.1186/s13742-015-0092-3

 received in 2015-02-06, accepted in 2015-10-27,  发布年份 2015

【 摘 要 】

Background

Semantic 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.

Findings

This 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 complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration.

Conclusions

The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.

【 授权许可】

   
2015 Aranguren and Wilkinson.

【 图 表 】

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