Title |
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker
|
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Published in |
Giga Science, December 2015
|
DOI | 10.1186/s13742-015-0092-3 |
Pubmed ID | |
Authors |
Mikel Egaña Aranguren, Mark D. Wilkinson |
Abstract |
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. 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. 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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 2 | 12% |
Japan | 1 | 6% |
Netherlands | 1 | 6% |
United States | 1 | 6% |
Australia | 1 | 6% |
Hong Kong | 1 | 6% |
France | 1 | 6% |
Spain | 1 | 6% |
Unknown | 8 | 47% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 12 | 71% |
Scientists | 4 | 24% |
Science communicators (journalists, bloggers, editors) | 1 | 6% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Japan | 1 | 3% |
Sweden | 1 | 3% |
Canada | 1 | 3% |
Unknown | 37 | 93% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 10 | 25% |
Student > Ph. D. Student | 7 | 18% |
Student > Bachelor | 5 | 13% |
Professor > Associate Professor | 4 | 10% |
Professor | 3 | 8% |
Other | 10 | 25% |
Unknown | 1 | 3% |
Readers by discipline | Count | As % |
---|---|---|
Computer Science | 11 | 28% |
Agricultural and Biological Sciences | 11 | 28% |
Biochemistry, Genetics and Molecular Biology | 5 | 13% |
Engineering | 4 | 10% |
Pharmacology, Toxicology and Pharmaceutical Science | 1 | 3% |
Other | 5 | 13% |
Unknown | 3 | 8% |