Talks, preprints, papers, and a leave of absence

This blog has been a bit quieter than usual in the year 2021, not because of the thing that messes everything else up in the world, but because o2r team member Daniel has been focussing on wrapping up his PhD thesis (it’s done!) and took a leave of absence 👶. Most of the activities below have been shared via the project’s Twitter feed, but we’d like to catch up the blog, too, and make a little announcement at the end. So with no further ado, here are events and publications of the last 8+ months:

Talks

o2r team members were given several opportunities to present work stemming from the project at conferenes and workshops.

• Sebastian presented the tool geoextent in the submission Exploring Research Data Repositories with geoextent at EarthCube 2021, see archived notebook and the workshop proceedings.

  It was great to participate in a scientific event that invited submissions of computational notebooks as the item of publication.

• Daniel presented the CODECHECK and Reproducible AGILE initiatives as well as the o2r approach to sharing computational workflows at several events with, admittedly, similar titles:
  • Code execution during peer review at Collaborations Workshop 2022, see slides and recording
  • Code Execution and Code Review in the Scholarly Communication Process at Mannheim Open Science Meetup on 2021-07-28, see slides
  • Executing workflows during peer review for transparency, reproducibility, and reusability at _Thüringer FDM-Tage 2021_organised by Thüringer Kompetenznetzwerk Forschungsdatenmanagement on 2021-06-23, see https://doi.org/10.5281/zenodo.5006378 and slides
• Daniel gave a talk on Rractical reproducibility and reproducibility vs. peer review at Spatial Data Science Hangout organised by the Center for Spatial Studies at UCSB on 2021-05-20, see slides

Preprints, abstracts, reports & postprints

A chapter of Daniel’s PhD thesis was published as a preprint:

Nüst, Daniel. 2021. A Web service for executable research compendia enables reproducible publications and transparent reviews in geospatial sciences. Zenodo. doi: 10.5281/zenodo.4818119

Daniel had the amazin opportunity to contribute to a Knowledge Exchange activity on Publishing Reproducible Research Outputs. Even though he is not an author, we want to point out the excellent reports from the group:

The Art of Publishing Reproducible Research Outputs: Supporting emerging practices through cultural and technological innovation. Chiarelli A, Loffreda, Lucia, Johnson R. 2021. Zenodo. https://doi.org/10.5281/zenodo.5521076

See also the executive summary if you are in a hurry.

As a continuation of the activities in Reproducible AGILE, Daniel contributed to a conference abstract on Reproducible graduate theses in GIScience with Carlos Granell and Rusne Sileryte, which was presented at Research Reproducibility 2020, University of Florida, on 2020-12-02, https://doi.org/10.17605/OSF.IO/WCEXY, see also slides.

And finally, the embargo period of a non-OA article by Daniel ended and he depsited the AAM as a postprint on EarthArXiv:

Practical Reproducibility in Geography and Geosciences. Nüst D, Pebesma E. 2022. EarthArXiv. https://doi.org/10.31223/X5XH0Z

Papers

The assessment of the reproducibility of GIScience conference papers was continued for the GIScience conference series, and former team member Markus was also on board again. We are very happy that this paper won the Best Paper award at the GIScience conference 2021!

Reproducible Research and GIScience: An Evaluation Using GIScience Conference Papers. Ostermann FO, Nüst D, Granell C, Hofer B, Konkol M. 2021. https://doi.org/10.4230/LIPIcs.GIScience.2021.II.2; preprint

Daniel presents a non-technology driven approach to reproducibility in this collaboration with Stephen Eglen:

CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility. Nüst D and Eglen SJ. [version 2; peer review: 2 approved]. F1000Research 2021, 10:253. https://doi.org/10.12688/f1000research.51738.2; preprint

The work was also featured on the F1000 blog here.

Daniel contributed to the following review article on metadata - thanks Jeremy for an outstanding job and the opportunity to take part!

The role of metadata in reproducible computational research. Leipzig J, Nüst D, Hoyt CT, Ram K, Greenberg J Article(journal). Patterns. 2021. https://doi.org/10.1016/j.patter.2021.100322; preprint

What if the o2r system is not flexible enough but you want to use containers to packaeg your data science workflow?

Ten simple rules for writing Dockerfiles for reproducible data science. Nüst D, Sochat V, Marwick B, Eglen SJ, Head T, Hirst T, Evans BD. PLOS Computational Biology. 2020. https://doi.org/10.1371/journal.pcbi.1008316

New team member

The o2r project is excited to have found a new team member to continue making research more reproducible, and to take some new directions, too. We welcome Eftychia Koukouraki to the team! She joins us after graduating from the Erasmus Mundus Masters in Geospatial Technologies as a member of the SITCOM lab. Before joining the exciting field of Geoinformatics, she worked in the industry as a Software Engineer and she also holds a Diploma in Electrical and Computer Engineering.

Great to have you on board, Eftychia - looking forward to see where you take the project!