#GenR Software Citation Round-up

A concluding summary of headline issues from the Open Science theme of ‘software citation’. Software citation is an important building block in the future of Open Science and has run as Generation R’s launch editorial theme. As with all of the topics of focus on Gen R editorially the issue will be revisited on regular occasions as major developments occur.

What is intrinsically important about software citation?

For the main part it would appear to be the case that until recently no one had indexed, or cataloged, research software. If we compared this situation to the cataloging of literature, and somehow nobody had cataloged publications for the last fifty years, then this would just be unimaginable. But for software this has been the case — for the last half-century there has been virtually no widespread and systematic indexing of software, or its citation in literature. There are exceptions, and the Astrophysics Source Code Library is such an exception and worthy of mention, started in 1999. (ASCL >1999)

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Beyond #FakeScience: How to Overcome Shallow Certainty in Scholarly Communication

Bad science journals – nothing new here

Science journalism in Germany in the last days was awash with a report on “predatory publishers” and an integrity ‘crisis’ for German science. Journalists from regional media outlets, WDR, NDR, and Süddeutsche Zeitung, in collaboration with some international partners (e.g., Le Monde) released new information (overview and links by ARD Tagesschau, in German) showing that some authors from esteemed research institutes in Germany previously had articles published by journals who apply next to no peer review on article submissions.

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Make Your Code Citable Using GitHub and Zenodo: A How-to Guide

This how-to guide is designed for researchers who want to create and re-use GitHub-based repositories in academic literature.

Open Science MOOC

The following guide has been made by the Open Science MOOC as part of preparation work on its first module release ‘Open Research Software and Open Source‘. The Open Science MOOC is made by an international volunteer group of over a hundred contributors, which you are free to join.

Gen R is a partner contributor to Open Science MOOC and over time as our editorial paths cross we will look to make a variety of contributions to the MOOC as a free and open learning resource for all.

Software Citation

It’s hard to overstate how important it is to have a record of what software has been produced, and also how little has been done in the past to create such indexes and catalogs of software. It’s like no one cataloged books for the last half-century and only now retrospectively took up the task.

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Software Citation Implementation in Astronomy

Image: Jupiter’s southern hemisphere was captured by NASA’s Juno spacecraft on the outbound leg of a close flyby of the gas-giant planet, 11:31 p.m. PDT on May 23, 2018. Image credit: NASA/JPL-Caltech/SwRI/MSSS/Kevin M. Gill. See: https://www.jpl.nasa.gov/spaceimages/details.php?id=PIA22425

This week’s post is a repost of a summary of a meeting held at the 231st American Astronomical Society (AAS) meeting in National Harbor, Maryland, USA, January 2018. The original summary, prepared by Daina Bouquin and Arfon Smith, is on GitHub, and is reproduced here with permission.


Software citation is foundationally important to the future of astronomy. Deep intellectual contributions are being made by people creating software to enable scientific research, and it is essential that software creators are encouraged to create these valuable resources. Efforts to help authors receive proper academic credit will allow them to prioritize writing software valuable for the astronomy community within their current profession or the ability to focus their whole career on it. With these facts in mind, on January 11, 2018 a “splinter meeting” was held at the 231st Meeting of the AAS that focused on implementing the FORCE11 Software Citation Principles (Appendix A) in Astronomy.

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Open Science #Barcamp: Software Citation

Image: Barcamp Open Science, Berlin, March 2018. Photo credits: Bettina Ausserhofer. All photos are also published at Wiki Commons under the CC BY 4.0 license.

A report from the barcamp session on software citation at Barcamp Open Science, Berlin, March 2018.

The Barcamp Open Science organized by the Leibniz Research Alliance Science 2.0 and hosted by Wikimedia Deutschland was designed as a pre-event before the two day Open Science Conference. The Barcamp offers a space for discussion, for developing new ideas and knowledge exchange on experiences and best practices in Open Science for researchers and practitioners from various backgrounds, with an emphasis on bringing together novices and experts.

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Software Preservation: A Stepping Stone for Software Citation

The Software Heritage archive growth graph (view live on 

In recent years software has become a legitimate product of research gaining more attention from the scholarly ecosystem than ever before, and researchers feel increasingly the need to cite the software they use or produce. Unfortunately, there is no well established best practice for doing this, and in the citations one sees used quite often ephemeral URLs or other identifiers that offer little or no guarantee that the cited software can be found later on.

But for software to be findable, it must have been preserved in the first place: hence software preservation is actually a prerequisite of software citation.

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Concrete Advice for FAIR Software

Video screen grab from The Leibniz “Mathematical Modeling and Simulation” (MMS) Days 2018 Leipzig, Feb / Mar 2018. (The video can be viewed at the bottom of the article)

This post was originally published in German on the TIB Blog (March 21.2018)

Findability Through Persistent Identifiers

In addition to implementing the FAIR Data Principles for research data there is a need to support the sustainable development, use, and publication of research software. This blog post represents an interim status of the development of these competences.

In addition, it shall introduce a series of articles, which similarly to the already explained FAIR Data Principles for research data (Kraft 2017) will recommend: concrete examples and actions to scientific software projects, summarizes specialist literature (see the bibliography), and also sets goals for our own software projects and those we supports.

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