Using Jupyter for reproducible scientific workflows

Marijan Beg, Juliette Belin, Thomas Kluyver, Alexander Konovalov*, Min Ragan-Kelley, Nicolas Thiery, Hans Fangohr

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)
18 Downloads (Pure)

Abstract

Literate computing has emerged as an important tool for computational studies and open science, with growing folklore of best practices. In this work, we report two case studies - one in computational magnetism and another in computational mathematics - where a dedicated software was exposed into the Jupyter environment. This enabled interactive and batch computational exploration of data, simulations, data analysis, and workflow documentation and outcome in Jupyter notebooks. In the first study, Ubermag drives existing computational micromagnetics software through a domain-specific language embedded in Python. In the second study, a dedicated Jupyter kernel interfaces with the GAP system for computational discrete algebra and its dedicated programming language. In light of these case studies, we discuss the benefits of this approach, including progress towards more reproducible and re-usable research results and outputs, notably through the use of infrastructure such as JupyterHub and Binder.

Original languageEnglish
Article number9325550
Pages (from-to)36-46
Number of pages11
JournalComputing in Science and Engineering
Volume23
Issue number2
Early online date15 Jan 2021
DOIs
Publication statusPublished - Mar 2021

Keywords

  • Jupyter

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