Interactive notebooks: Sharing the code

Shen, Helen C.

doi:10.1038/515151ax

Cited by 64 publications

(72 citation statements)

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“…Recent developments on interactive notebooks [She14] have set a trend towards reproducible and shareable data analytics. InsideInsights continues this trend by allowing the creation of data‐driven reports that can be accessed by many different users, thereby making data analytics accessible to a wider audience.…”

Section: Discussion and Future Workmentioning

confidence: 99%

InsideInsights: Integrating Data‐Driven Reporting in Collaborative Visual Analytics

Mathisen

Horak

Klokmose

et al. 2019

Computer Graphics Forum

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Analyzing complex data is a non‐linear process that alternates between identifying discrete facts and developing overall assessments and conclusions. In addition, data analysis rarely occurs in solitude; multiple collaborators can be engaged in the same analysis, or intermediate results can be reported to stakeholders. However, current data‐driven communication tools are detached from the analysis process and promote linear stories that forego the hierarchical and branching nature of data analysis, which leads to either too much or too little detail in the final report. We propose a conceptual design for integrated data‐driven reporting that allows for iterative structuring of insights into hierarchies linked to analytic provenance and chosen analysis views. The hierarchies become dynamic and interactive reports where collaborators can review and modify the analysis at a desired level of detail. Our web‐based InsideInsights system provides interaction techniques to annotate states of analytic components, structure annotations, and link them to appropriate presentation views. We demonstrate the generality and usefulness of our system with two use cases and a qualitative expert review.

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Section: Discussion and Future Workmentioning

confidence: 99%

InsideInsights: Integrating Data‐Driven Reporting in Collaborative Visual Analytics

Mathisen

Horak

Klokmose

et al. 2019

Computer Graphics Forum

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“…The record of origin or provenance of the results of published articles is often only provided at a high level in current articles, missing important details due to lack of space, or to the ambiguity inherent in natural language text. Interactive notebooks are gaining popularity, including iPhython Notebook for Python [ Shen , ], Sweave for R in Latex [ Leisch , ; Falcon , ], and the Computable Document Format for Mathematica [ Wolfram , ]. Executable papers are designed to enable readers to run experiments [ Koop et al ., ].…”

Section: Background and Motivationmentioning

confidence: 99%

Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance

Gil

David

Demir

et al. 2016

Earth and Space Science

156

153

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Geoscientists now live in a world rich with digital data and methods, and their computational research cannot be fully captured in traditional publications. The Geoscience Paper of the Future (GPF) presents an approach to fully document, share, and cite all their research products including data, software, and computational provenance. This article proposes best practices for GPF authors to make data, software, and methods openly accessible, citable, and well documented. The publication of digital objects empowers scientists to manage their research products as valuable scientific assets in an open and transparent way that enables broader access by other scientists, students, decision makers, and the public. Improving documentation and dissemination of research will accelerate the pace of scientific discovery by improving the ability of others to build upon published work.

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“…A wide body of literature has been published in high‐impact scientific journals over the past few years on the general subject of promoting transparent and trustworthy science results. Much of the discussion has revolved around the importance of scientific reproducibility [ Ioannidis et al ., ; Hutson , ; Mesirov , ; Jasny et al ., ; Russell , ; Collins and Tabak , ; Buck , ] and on the need for data sharing [ Kattge et al ., ; Scientific Data , ] and software sharing [ Barnes , ; Ince et al ., ; Easterbrook , ; Nature , ; Nature Geoscience , ; Shen , ; Hey and Payne , ]. One of the outcomes of these discussions—as well as a contributor to its liveliness—has been new government mandates on increased sharing of digital products resulting from publicly funded research [e.g., Holdren , ].…”

Section: Introductionmentioning

confidence: 99%

“…Such information is typically embedded in the text of research papers with the inherent ambiguity of natural languages [ Ince et al ., ] and with the restricted length of the “Methods” section. Yet the explicit computational representation of research methods is increasingly becoming practical thanks to tools such as interactive notebooks [ Shen , ]. Finally, open access to digital research products implies careful choice of licenses to clarify permissions and restrictions intended by the authors [ Stodden , ].…”

Section: Introductionmentioning

confidence: 99%

An introduction to the special issue on Geoscience Papers of the Future

David

Gil

Duffy

et al. 2016

Earth and Space Science

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Advocates of enhanced quality for published scientific results are increasingly voicing the need for further transparency of data and software for scientific reproducibility. However, such advanced digital scholarship can appear perplexing to geoscientists that are seduced by the concept of open science yet wonder about the exact mechanics and implications of the associated efforts. This special issue of Earth and Space Science entitled "Geoscience Papers of the Future" includes a review of existing best practices for digital scholarship and bundles a set of example articles that share their digital research products and reflect on the process of opening their scientific approach in a common quest for reproducible science.

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Interactive notebooks: Sharing the code

Cited by 64 publications

References 0 publications

InsideInsights: Integrating Data‐Driven Reporting in Collaborative Visual Analytics

InsideInsights: Integrating Data‐Driven Reporting in Collaborative Visual Analytics

Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance

An introduction to the special issue on Geoscience Papers of the Future

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