In academia, the published paper is the currency of the realm. However, reports of a lack of reproducibility and transparency have led funders and others to require open data and code as part of their published outputs, but current academic publishing systems still cannot support the solutions that technology has enabled, such as the Jupyter Notebook. Mark Hahnel and Marius Tulbure discuss the opportunities for Jupyter notebooks to be the final output of academic research, arguing that Jupyter could help disrupt the inefficiencies in cost and scale of open access academic publishing.
While working with publishers at figshare, Mark and Marius received several enquiries from authors about supporting executable notebooks. As a result, the company has enabled the publishing of .ipynb files directly to figshare with a file preview in the browser. Mark and Marius explain what is needed for the Jupyter notebooks to be recognized in this format and how credit can be assigned. They also demonstrate working examples and discuss the role peer review might play. Mark and Marius then turn to the work they have been doing to enable FAIR (findable, accessible, interoperable, and reusable) principles using the suite of Jupyter tools with Jupyter notebooks and showcase an executable paper with reproducible data that enables interactive hacking.
Mark Hahnel is the founder of figshare, an open data tool that allows researchers to publish all of their data in a citable, searchable, and sharable manner. Mark is passionate about open science and the potential it has to revolutionize the research community. He’s fresh out of academia, having just completed his PhD in stem cell biology at Imperial College London. Mark also studied genetics in Newcastle and Leeds.
©2017, O'Reilly Media, Inc. • (800) 889-8969 or (707) 827-7019 • Monday-Friday 7:30am-5pm PT • All trademarks and registered trademarks appearing on oreilly.com are the property of their respective owners. • firstname.lastname@example.org