2016-05-18 Make Research Reproducible Again

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On 2016-05-18, Stian Soiland-Reyes presented Make Research Reproducible Again at the ELIXIR organized hackathon Tools, Workflow and Workbenches at Institut Pasteur in Paris.

The hackathon had a very strong focus and presence for both bio.tools and Common Workflow Language, one of the activities was to explore how CWL metadata profile could relate to Research Object model, Debian’s package descriptions, RDF, schema.org and provenance.

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BagIt for transferring and archiving Research Objects

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BagIt is an Internet Draft that specifies a file system structure for transferring and archiving a collection of files, including their checksums and brief metadata. BagIt is commonly used by digital library communities for archival purposes, and is mandated by the Library of Congress for digital preservation.

Research Object bundles are structured ZIP-files for serializes a Research Objects, embedding some or all of its resources within the ZIP file, and list the RO content in a manifest, in addition to embedding and referencing annotations and provenance.

While BagIt and RO Bundle might at first seem to provide similar functionalies, the two approaches are complementary in the sense that BagIt focuses on the transfer and consistency checks, recording checksums for resources and their file sizes, while RO Bundles focus on the metadata, provenance and annotations about the resources, relating them to each other.

Research Object BagIt archive defines a profile for a BagIt bag to also be a Research Object. This approach builds on the RO Bundle structure, but modifies it to also be compliant with BagIt.


Research Objects at BOSC

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Norman Morrison presented Research Objects at BOSC including work on ‘Research Objects in the wild’, where Research Objects supported a reproducibility case study that was recently publish in PLOS One. This work was also presented at BOSC by Alejandra González-Beltrán from the ISA-team and you can get the slides here.

You can read more about the BOSC conference in Scott Edmunds excellent blog post ‘Open Bioinformatics in The Irish Free Software State‘.


Why publish and be so damned hard to find?

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Chris Parr from Times Higher Education Interviewed Prof Carole Goble at JISC Digifest. You can read and listen to Carole’s views on the lack of transparency about academic research methods by clicking on the links below.

“Outdated practices and lack of simplicity result in ‘unfindable’ work, Carole Goble tells Jisc Digital Festival”