2017-09-27 eLife Reproducible Portable Publications

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On 2017-09-27 I met with Naomi Penfold and Giuliano Maciocci from the journal eLife, Oliver Buchtala and Michael Aufreiter working on Substance, and Nokome Bentley doing Stencila. Our topic was the eLife/Substance/Stencila collaboration for a Reproducible Document Stack, and how that can relate to Research Objects and other Scholarly HTML initiatives. This blog post gives… Read more »

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… Read more »


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Wikipedia: GitHub is a Git repository web-based hosting service which offers all of the functionality of Git as well as adding many of its own features. Unlike Git, which is strictly a command-linetool, Github provides a web-based graphical interface and desktop as well as mobile integration. It also provides access control and several collaboration features such as wikis, task management, and bug tracking and feature requests for every project.

OKF Ckan

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From Wikipedia: The Comprehensive Knowledge Archive Network (CKAN) is a web-based open source data management system for the storage and distribution of data, such as spreadsheets and the contents of databases. It is inspired by the package management capabilities common to open source operating systems like Linux, and is intended to be the “apt-get of Debian for data”. Its code base is maintained by the Open… Read more »


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Projects.ac is a commercial application developed and released by digital science. The goal of the application is to support the academic researcher in managing collections of content that relate to projects or studies. A key feature of projects is a timeline that displays a trace of the provenance for a project as a series of… Read more »

OKF Data Packages

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A Data Package (or DataPackage) is a simple way of “packaging” up data. To create a Data Package, all you need to do is place a “descriptor” file named datapackage.json in the top-level directory of your set of data files. Why Data Packages? How Can They Help? Imagine a situation such as the following: You have a… Read more »

Clinicalcodes.org Exchange

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The clinicalcodes.org repository holds code lists for published electronic medical record studies (i.e. the coded descriptions of study cohorts). The goal of clinicalcodes.org is support replication of previously published studies. Using the Research Object model, an export of a study packages codes, study, and metadata together to support exchange. An Example RO exported in this manner… Read more »

Code as a Research Object

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Code as a Research Object is a joint initiative between the Mozilla Science Lab, figshare and GitHub. figshare and GitHub two leading repositories for data and code. The project has built a bridge to allow users to push code from their GitHub repository to figshare, providing a Digital Object Identifier for the code.