Opening Reproducible Research (o2r)
- Period
- Status
- Finished
- Project Number
- TR 864/6-1; KR 3930/3-1; PE 1632/10-1
Description
Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. When science transforms to open access we mean access to papers, research data being collected, data being generated, access to the procedures carried out in the research paper, even to the computational environment that was used, in order to reproduce and inspect the findings in the paper.Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method. For many sciences the reproduction involves the replication of an experimental set up, e.g. in the lab or a field mission to collect data. Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are completely carried out computationally.In this proposal Opening Reproducible Research (ORR) we directly aim for the main aspects of open access, by improving the exchange of, by facilitating productive access to and by simplifying reuse of research results that are published over the Internet. The experimentally oriented proposal ORR aims at both the publication process (technische und organisatorische Aspekte des Publikationsprozesses) and the reuse of publications (Absichern der möglichst umfassenden Nachnutzbarkeit der Publikationen), but combines these goals by setting a clear innovation in the area of reproducible research, a goal that has extraordinary meaning for scientific publication. Central to the proposal is a new form for creating and providing research results, the executable research compendium (ERC), which not only enables third parties to reproduce the original research and hence recreate the original research results (figures, tables), but also facilitates interaction with them and the recombination of them with new data or methods. The container format that specifies the ERC will store all information required by different applications (e.g. one-click reproduce, long-term archive, research information systems, discovery purposes) and thus guarantees use independent from original information systems. Building on existing open standards and software, this project will develop standards and tools for ERCs and demonstrate and evaluate these based on fully fledged case studies, initially taken from the geosciences domain. ORR will make a step forward towards executable papers as a new standard in scientific publication. Persons
Publications
- Nüst, Daniel. . “Infrastructures and Practices for Reproducible Research in Geography, Geosciences, and GIScience.” Dissertation thesis, Universität Münster. doi: 10.5281/zenodo.4768096.
- Nüst, Daniel. . preprint, A Web service for executable research compendia enables reproducible publications and transparent reviews in geospatial sciences Zenodo. doi: 10.5281/zenodo.4818119.
- Nüst, D, Ostermann, FO, Sileryte, R, Hofer, B, Granell, C, Teperek, M, Graser, A, Broman, K, and Hettne, K. . AGILE Reproducible Paper Guidelines OSF. doi: 10.17605/OSF.IO/CB7Z8.
- Konkol, M., Kray, C., and Suleiman, J. . “Creating interactive scientific publications using bindings.” Proceedings of the ACM on Human-Computer Interaction 3 (EICS). doi: 10.1145/3331158.
- Nüst, Daniel, Lohoff, Lukas, Einfeldt, Lasse, Gavish, Nimrod, Götza, Marlena, Tariq, Jaswal Shahzeib, Khalid, Salman, Meierkort, Laura, Mohr, Matthias, Rendel, Clara, and Antonia, van Eek. . “Guerrilla Badges for Reproducible Geospatial Data Science.” in Accepted Short Papers and Posters from the 22nd AGILE Conference on Geo‐information Science, edited by P Kyriakidis, D Hadjimitsis, D Skarlatos and A Mansourian. Limassol, Cyprus: Springer. doi: 10.31223/osf.io/xtsqh.
- Nüst, Daniel, Boettiger, Carl, and Marwick, Ben. . How to Read a Research Compendium https://arxiv.org/abs/1806.09525: arXiv.
- Nüst, Daniel. . Reproducibility Service for Executable Research Compendia: Technical Specifications and Reference Implementation doi: 10.5281/zenodo.2203844.
- Konkol, M, and Kray, C. . “In-depth examination of spatiotemporal figures in open reproducible research.” Cartography and Geographic Information Science 2018. doi: 10.1080/15230406.2018.1512421.
- Konkol, M, Kray, C, and Pfeiffer, M. . “Computational reproducibility in geoscientific papers: Insights from a series of studies with geoscientists and a reproduction study.” International Journal of Geographical Information Science 2018. doi: 10.1080/13658816.2018.1508687.
- Nüst, Daniel, Granell, Carlos, Hofer, Barbara, Konkol, Markus, Ostermann, Frank O, Sileryte, Ruse, and Cerutti, Valentina. . “Reproducible research and GIScience: an evaluation using AGILE conference papers.” PeerJ 6: e5072.. doi: 10.7717/peerj.5072.
- Nüst, Daniel Bartoschek Thomas. . “Open Environmental Data Analysis.” contribution to the EGU General Assembly 2018, Vienna, Austria doi: 10.5281/zenodo.1217911.
- Nüst, Daniel, Boettiger, Carl, and Eddelbuettel, Dirk. . “rocker/geospatial: a flexible runtime environment for geoscientific data analysis.” contribution to the EGU General Assembly 2018, Vienna, Austria doi: 10.5281/zenodo.1216750.
- Nüst, Daniel, Granell, Carlos, Hofer, Barbara, Konkol, Markus, Ostermann, Frank, Sileryte, Rusne, and Cerutti, Valentina. . Peerj Preprints, Vol. 6:e26561v1, Reproducible research and GIScience: an evaluation using AGILE conference papers doi: 10.7287/peerj.preprints.26561v1.
- Konkol, M, Kray, C, and Pfeiffer, M. . The State of Reproducibility in the Computational Geosciences doi: 10.17605/OSF.IO/KZU8E.
- Konkol, M, and Kray, C. . In-depth examination of spatio-temporal figures in open reproducible research doi: 10.17605/OSF.IO/Q53M8.
- Konkol, M. in Kürze. “Reproducible research bindings.” contribution to the European Geosciences Union General Assembly 2018, Wien, Österreich
- Nüst, Daniel, Schutzeichel, Marc, and Konkol, Markus. . Opening Reproducible Research: a research project website and blog doi: 10.5281/zenodo.1485437.
- Granell, Carlos, Nüst, Daniel, Ostermann, Frank O, and Sileryte, Rusne. . “Reproducible Research is like riding a bike.” PeerJ Preprints 6 (e27216v1). doi: 10.7287/peerj.preprints.27216v1.
- Nüst, Daniel, and Schutzeichel, Marc. . “An Architecture for Reproducible Computational Geosciences.” in Societal Geo-Innovation doi: 10.5281/zenodo.1478542.
- Konkol, Markus, Nüst, Daniel, Schutzeichel, Marc, Pebesma, Edzer, Kray, Christian, Przibytzin, Holger, and Lorenz, Jörg. . “Opening reproducible research (o2r).” contribution to the Open Science Conference, Berlin, Germany
- Nüst, D, Konkol, M, Pebesma, E, Kray, C, Schutzeichel, M, Przibytzin, H, and Lorenz, J. . “Opening the Publication Process with Executable Research Compendia.” D-Lib Magazine 23. doi: 10.1045/january2017-nuest.
- Nüst, Daniel. . “Executable research compendia in geoscience research infrastructures.” in Vol. EGU2017-7215 of Geophysical Research Abstracts
- Knoth, C, and Nüst, D. . “Reproducibility and Practical Adoption of GEOBIA with Open-Source Software in Docker Containers.” Remote Sensing 9 (3). doi: 10.3390/rs9030290.
- Appel, Marius, Nüst, Daniel, and Pebesma, Edzer. . “Reproducible Earth observation analytics: challenges, ideas, and a study case on containerized land use change detection.” contribution to the EGU General Assembly 2017, Vienna, Austria
- Knoth, Christian Nüst Daniel. . “Enabling Reproducible OBIA with Open-Source Software in Docker Containers.” contribution to the GEOBIA 2016: Solutions & Synergies, Enschede, The Netherlands doi: 10.3990/2.456.
- Stasch, Christoph, and Nüst Daniel, Pross Benjamin. . “Sharing environmental models: An Approach using GitHub repositories and Web Processing Services.” in Vol. 18 of Geophysical Research Abstracts, edited by European Geophysical Union.
- Nüst, Daniel, Konkol, Markus, Pebesma, Edzer, Kray, Christian, Klötgen, Stephanie, Schutzeichel, Marc, Lorenz, Jörg, Przibytzin, Holger, and Kussmann, Dirk. . “Opening Reproducible Research.” in Vol. 18 of Geophysical Research Abstracts, edited by European Geophysical Union.