Archives des mots-clés : Markus Konkol

Publishing computational research — A review of infrastructures for reproducible and transparent scholarly communication

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Authors : Markus Konkol, Daniel Nüst, Laura Goulier

Funding agencies increasingly ask applicants to include data and software management plans into proposals. In addition, the author guidelines of scientific journals and conferences more often include a statement on data availability, and some reviewers reject unreproducible submissions.

This trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results in their scientific papers.

Still, publishing reproducible articles is a demanding task and not achieved simply by providing access to code scripts and data files. Consequently, several projects develop solutions to support the publication of executable analyses alongside articles considering the needs of the aforementioned stakeholders.

The key contribution of this paper is a review of applications addressing the issue of publishing executable computational research results. We compare the approaches across properties relevant for the involved stakeholders, e.g., provided features and deployment options, and also critically discuss trends and limitations.

The review can support publishers to decide which system to integrate into their submission process, editors to recommend tools for researchers, and authors of scientific papers to adhere to reproducibility principles.

URL : https://arxiv.org/abs/2001.00484

Reproducible research and GIScience: an evaluation using AGILE conference papers

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Authors : Daniel Nüst​, Carlos Granell, Barbara Hofer, Markus Konkol, Frank O Ostermann, Rusne Sileryte, Valentina Cerutti

The demand for reproducibility of research is on the rise in disciplines concerned with data analysis and computational methods. In this work existing recommendations for reproducible research are reviewed and translated into criteria for assessing reproducibility of articles in the field of geographic information science (GIScience).

Using a sample of GIScience research from the Association of Geographic Information Laboratories in Europe (AGILE) conference series, we assess the current state of reproducibility of publications in this field. Feedback on the assessment was collected by surveying the authors of the sample papers.

The results show the reproducibility levels are low. Although authors support the ideals, the incentives are too small. Therefore we propose concrete actions for individual researchers and the AGILE conference series to improve transparency and reproducibility, such as imparting data and software skills, an award, paper badges, author guidelines for computational research, and Open Access publications.

URL : Reproducible research and GIScience: an evaluation using AGILE conference papers

DOI : https://doi.org/10.7287/peerj.preprints.26561v1

Opening the Publication Process with Executable Research Compendia

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Authors : Daniel Nüst, Markus Konkol, Marc Schutzeichel, Edzer Pebesma, Christian Kray, Holger Przibytzin, Jörg Lorenz

A strong movement towards openness has seized science. Open data and methods, open source software, Open Access, open reviews, and open research platforms provide the legal and technical solutions to new forms of research and publishing.

However, publishing reproducible research is still not common practice. Reasons include a lack of incentives and a missing standardized infrastructure for providing research material such as data sets and source code together with a scientific paper. Therefore we first study fundamentals and existing approaches.

On that basis, our key contributions are the identification of core requirements of authors, readers, publishers, curators, as well as preservationists and the subsequent description of an executable research compendium (ERC). It is the main component of a publication process providing a new way to publish and access computational research.

ERCs provide a new standardisable packaging mechanism which combines data, software, text, and a user interface description. We discuss the potential of ERCs and their challenges in the context of user requirements and the established publication processes.

We conclude that ERCs provide a novel potential to find, explore, reuse, and archive computer-based research.

DOI : https://doi.org/10.1045/january2017-nuest