ArticleGigaScience2015
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.
Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed.
- The role of metadata in reproducible computational research.Patterns (New York, N.Y.) · 2021Review
- Improving data workflow systems with cloud services and use of open data for bioinformatics research.Briefings in bioinformatics · 2018Review
- An architecture for genomics analysis in a clinical setting using Galaxy and Docker.GigaScience · 2017Article
- Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.Journal of integrative bioinformatics · 2017Article
- Science in the cloud (SIC): A use case in MRI connectomics.GigaScience · 2017Article
- Article
- GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.PloS one · 2016Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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 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.
conclusionsThe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.