24 Feb 2019 | Daniel Nüst
The o2r project website’s first entry Introducing o2r was published 1132 days ago.
Since then we’ve published short and long reports about events the o2r team participated in, advertised new scholarly publications we were lucky to have accepted in journals, and reported on results of workshops organised by o2r.
But there has also been some original content from time to time, such as the extensive articles on Docker and R, which received several updates over the last years (some still pending), on the integration of Stencila and Binder, or on writing reproducible articles for Copernicus Publications.
These posts are a valuable output of the project, and contribute to the scholarly discussion.
Therefore, when it came to writing a report on the project’s activities and outputs, it was time to consider the preservation of the project website and blog.
The website is built with Jekyll (with Markdown source files) and hosted with GitHub pages, but GitHub may disappear and Jekyll might stop working at some point…
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16 Feb 2019 | Daniel Nüst
The capabilities of containerisation and the concept of the Executable Research Compendium form the basis for o2r’s reproducibility service.
But the demonstration how latest technology may support a more open and transparent scholarly publication alone is only one half the battle.
Breakthroughs in tools and infrastructure must be accompanied by outreach activities to highlight the need for opening reproducible research to all stakeholders (scientists, editors, publishers, funding agencies).
That is why I was extremely glad to join some of the most renowned researchers of geography and GI Science at the “Replicability and Reproducibility Workshop” in Tempe, Arizona, on February 11 and 12, 2019.
The event was organised by the Spatial Analysis Research Center (SPARC) at Arizona State University (ASU).
The events featured…
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04 Feb 2019 | Daniel Nüst
[This article is cross posted-on the EGU GeoLog.]
Contemporary science faces many challenges in publishing results that are reproducible.
This is due to increased usage of data and digital technologies as well as heightened demands for scholarly communication.
These challenges have led to widespread calls for more research transparency, accessibility, and reproducibility from the science community.
This article presents current findings and solutions to these problems, including recent new software that makes writing submission-ready manuscripts for journals of Copernicus Publications a lot easier.…
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17 Dec 2018 | Markus Konkol, Daniel Nüst
A few weeks ago, a new journal article written by o2r team member Markus got published.
In our last article, we talked about the reproducibility of papers submitted to the AGILE conference.
We checked if the papers had materials attached and if these materials were complete.
The results were rather unfortunate.
In our newest article, we took one further step and tried to re-run the analyses of articles which had code and data in the supplements.
Markus Konkol, Christian Kray & Max Pfeiffer (2019). Computational reproducibility in geoscientific papers: Insights from a series of studies with geoscientists and a reproduction study, International Journal of Geographical Information Science, 33:2, 408-429, DOI: 10.1080/13658816.2018.1508687
The article builds upon our paper corpus for demonstrating the o2r platform.
Feel free to distribute this piece of research to whoever might be interested.
Feedback is always welcome.
Here is a non-specialist summary:
Recreating scientific data analysis is hard, but important.
To learn more about the state of reproducibility in geosciences, we conducted several studies.
We contacted over 150 geoscientists who publish and read articles based on code and data.
We learned that as readers they often would like to have access to these materials, but as authors they often do not have the time or expertise to make them available.
We also collected articles which use computational analyses and tried to execute the attached code.
This was not as easy as it sounds! We describe these numerous issues in a structured way and our experiences in this publication.
Some issues were pretty easy to solve, such as installing a missing library.
Others were more demanding and required deep knowledge of the code which is, as you might imagine, highly time consuming.
Further issues were missing materials (code snippets, data subsets) and flawed functionalities.
In some cases, we contacted the original authors who were, and this was a positive outcome, mostly willing to help.
We also compared the figures we got out of the code with those contained in the original article.
Bad news: We found several differences related to the design of the figures and results that deviated from those described in the paper.
OK, this is interesting, but why is it important?
We argue, a key advantage of open reproducible research is that you can reuse existing materials.
Apparently, this is usually not possible without some significant effort. Our goal is not to blame authors.
We are very happy that they shared their materials.
But they did that with a specific purpose in mind, i.e. making code and data available and reusable for others to build upon that.
One incentive in this context is an increased number of citations, one of the main currencies for researchers.
To facilitate that, we suggest some guidelines to avoid the issues we encountered during our reproducibility study, such as using Executable Research Compendia (ever heard of them? :)).
21 Nov 2018 | Daniel Nüst
This article reports on a project, integrating Stencila and Binder, which started at the eLife Innovation Sprint 2018. It has been cross-posted on multiple blogs (eLife Labs, Stencila, Jupyter). We welcome comments and feedback on any of them!
eLife, an open science journal published by the non-profit organisation eLife Sciences Publications from the UK, hosted the first eLife Innovation Sprint 2018 as part of their Innovation Initiative in Cambridge, UK:
“[..] a two-day gathering of 62 researchers, designers, developers, technologists, science communicators and more, with the goal of developing prototypes of innovations that bring cutting-edge technology to open research communication.”
One of the 13 projects at the excellently organised event was an integration of Binder and Stencila…
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