Using Jupyter for reproducible scientific workflows
File(s)
Accepted version
Author(s)
Type
Journal Article
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 domain-specific software was exposed to the Jupyter environment. This enables high level control of simulations and computation, interactive exploration of computational results, batch processing on HPC resources, and reproducible workflow documentation 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 toward more reproducible and reusable research results and outputs, notably through the use of infrastructure such as JupyterHub and Binder.
Date Issued
2021-03-01
Date Acceptance
2021-01-01
Citation
Computing in Science and Engineering, 2021, 23 (2), pp.36-46
ISSN
1521-9615
Publisher
Institute of Electrical and Electronics Engineers
Start Page
36
End Page
46
Journal / Book Title
Computing in Science and Engineering
Volume
23
Issue
2
Copyright Statement
Copyright © 2021 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Identifier
http://arxiv.org/abs/2102.09562v1
Subjects
Computer Science
Computer Science, Interdisciplinary Applications
Science & Technology
Technology
Publication Status
Published
Date Publish Online
2021-01-15