Resources for week 5

Resource Data Management

BMJV. „Verordnung über die Anwendung der Guten Klinischen Praxis bei der Durchführung von klinischen Prüfungen mit Arzneimitteln zur Anwendung an Menschen.“ Last accessed 03.11.2020, https://www.ethik.uni-jena.de/ethae_femedia/files/ethikkommission/gcp-verordnung.pdf.

CESSDA. Last accessed 03.11.2020, https://www.cessda.eu.

DARIAH-DE. „Digitale Forschungsinfrastruktur für die Geistes- und Kulturwissenschaften.“ https://de.dariah.eu/en/web/guest/home, last accessed 21.09.2020.

DARIAH-DE, “Forschungsdaten” (research data), https://de.dariah.eu/en/forschungsdaten, last accessed 26.08.2020.

Deutsche Forschungsgemeinschaft. „DFG Guidelines on the Handling of Research Data.“ DFG, 2015. https://www.dfg.de/download/pdf/foerderung/antragstellung/forschungsdaten/guidelines_research_data.pdf, Last accessed 03.11.2020..

DFG Guidelines on the Handling of Research Data, https://www.dfg.de/download/pdf/foerderung/antragstellung/forschungsdaten/guidelines_research_data.pdf, last accessed 26.08.2020.

Elsevier. „Sharing research data.“, https://www.elsevier.com/authors/author-services/research-data, Last accessed 03.11.2020.

European Commission, H2020 Programme. “Guidelines on FAIR Data Management in Horizon 2020.” Version 3.0. , http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-oa-datamgt_en.pdf Last accessed 03.11.2020.

European Commission, H2020 Programme. “Guidelines on FAIR Data Management in Horizon 2020.” Version 3.0., http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020-hi-oa-datamgt_en.pdf, Last accessed 07.10.2020.

Deutsche Forschungsgemeinschaft. „Leitlinien zum Umgang mit Forschungsdaten.” , http://www.dfg.de/download/pdf/foerderung/antragstellung/forschungsdaten/richtlinien_forschungsdaten.pdf, Last accessed 28.07.2020.

Hiemenz, Bea M. and Monika Kuberek: „Leitlinie? Grandsätze? Policy? Richtlinie? – Forschungsdaten-Policies an deutschen Universitäten.“ o-bib 5,2 (2018): pp. 1-13. https://doi.org/10.5282/o-bib/2018H2S1-13.

Humboldt-Universität zu Berlin. „Humboldt-Universität zu Berlin Research Data Management Policy.“ Berlin, 2014. https://hu.berlin/RDM-policy, Last accessed 03.11.2020.

Kindling, Maxi and Peter Schirmbacher. “Die digitale Forschungswelt‘ als Gegenstand der Forschung.“ Information – Wissenschaft & Praxis 64 (2013): pp. 127-136, p. 130. https://doi.org/10.1515/iwp-2013-0017. (transl. Maik Bierwirth)

List of research data policies by German universities and colleges:

forschungsdaten.org: „Data Policies“. Last accessed 28.07.2020.

Louise Corti, Veerle Van den Eynden, Libby Bishop and Matthew Woollard: Managing and Sharing Research Data: A Guide to Good Practice. Los Angeles, CA: SAGE, 2014.

Meyermann, Alexia: „Datenmanagement – Eine zentrale Voraussetzung für den Erfolg der Data Sharing-Idee in den Sozialwissenschaften.“ DSZ-BO Working Paper Series 2,7 (2012). http://www.uni-bielefeld.de/dsz-bo/pdf/2012-07-23_WP2_Datenmanagement.pdf. (transl.Maik Bierwirth), Last Accessed 27.10.2020.

Nosek, Brian A., George Alter, George C. Banks, Denny Borsboom, Sara D. Bowman, Steven J. Breckler, Stuart Buck et al.: „Promoting an open research culture.” Science 348, 6242 (2015): pp. 1422–1425. https://doi.org/10.1126/science.aab2374.

Piwowar, Heather, Roger S. Day and Douglas B. Fridsma: Sharing detailed research data is associated with increased citation rate. PloS one, 2,3, e308 (2007). https://doi.org/10.1371/journal.pone.0000308.

RDA Interest Group Active Data Management Plans. https://www.rd-alliance.org/node/9136/outputs, Last accessed 12.06.2020.

Springer Nature. „Research Data Policies.“ https://www.springernature.com/gp/authors/research-data-policy/journal-policies/15369670, Last accessed 16.01.2019,

UK Data Service. „Research data lifecycle.“ https://ukdataservice.ac.uk/data-skills-resource/research-data-lifecycle/, Accessed on 18.05.2018.

Verband Forschungsdaten Bildung. „Checklist zur Erstellung eines Datenmanagementplans in der empirischen Bildungsforschung.“ Version 1.1. fdbinfo Nr. 2 (2015). https://www.forschungsdaten-bildung.de/files/fdbinfo_2.pdf, Last accessed 26.02.2019.

VolkswagenStiftung. „Information Open Access – Open Data – Open Source.” https://www.volkswagenstiftung.de/sites/default/files/documents/Open_Science_Policy_and_Implementation_Volkswagen_Foundation.pdf, Last accessed 09.07.2020,

Wiley. „Sharing and Citing your Research Data.” https://authorservices.wiley.com/author-resources/Journal-Authors/licensing-open-access/openaccess/data-sharing.html, Last accessed 03.11.2020.

Open Reproducible Research

Last access of all URLs: 11th April 2021.

Alston, J. & Rick, J. (2020). A Beginner’s Guide to Conducting Reproducible Research. http://dx.doi.org/10.32942/osf.io/h5r6n.

Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature 533, 452–454. https://doi.org/10.1038/533452a.

Binder (2017). User guide – Get started. https://mybinder.readthedocs.io/en/latest/index.html#get-started.

Brinckman, A. et al. (2019). Computing environments for reproducibility: Capturing the “Whole Tale.” Future Generation Computer Systems, 94, 854–867. http://dx.doi.org/10.1016/j.future.2017.12.029.

Buckheit, J.B. & Donoho, D.L. (1995). WaveLab and Reproducible Research. Lecture Notes in Statistics, 55–81. http://dx.doi.org/10.1007/978-1-4612-2544-7_5.

Chawla, D. S. (2020) Critiqued coronavirus simulation gets thumbs up from code-checking efforts Nature 582, 323-324. https://doi.org/10.1038/d41586-020-01685-y.

Culina, A., van den Berg, I., Evans, S., Sánchez-Tójar, A. (2020) Low availability of code in ecology: A call for urgent action. PLOS Biology 18(7): e3000763. https://doi.org/10.1371/journal.pbio.3000763.

Davies, N. G., Kucharski, A. J., Eggo, R. M., Gimma, A., Edmunds, W. J., Jombart, T., … & Liu, Y. (2020). Effects of non-pharmaceutical interventions on COVID-19 cases, deaths, and demand for hospital services in the UK: a modelling study. The Lancet Public Health, 5(7), e375-e385. https://doi.org/10.1016/S2468-2667(20)30133-X.

Gil, Y., David, C. H., Demir, I., Essawy, B. T., Fulweiler, R. W., Goodall, J. L., … & Yu, X. (2016). Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance. Earth and Space Science, 3(10), 388–415. https://doi.org/10.1002/2015ea000136.

GitHub. Choose an open source license. https://choosealicense.com/.

Eglen, S. J. (2020). CODECHECK certificate 2020-008. Zenodo. https://doi.org/10.5281/zenodo.3746024.

Goodman, S. N., Fanelli, D. & Ioannidis, J.P.A. (2016). What does research reproducibility mean? Science Translational Medicine, 8(341). http://dx.doi.org/10.1126/scitranslmed.aaf5027.

Hasselbring, W., Carr, L., Hettrick, S., Packer, H. & Tiropanis, T. (2020). Open Source Research Software. Computer, 53, 8, 84-88. https://doi.org/10.1109/MC.2020.2998235.

Hettne, K., Proppert, R., Nab, L., Rojas-Saunero, L. P., & Gawehns, D. (2020).

ReprohackNL 2019: how libraries can promote research reproducibility through community engagement. IASSIST Quarterly, 44(1-2), 1–10. https://doi.org/10.29173/iq977.

Hutson, M. (2018). Artificial intelligence faces reproducibility crisis. Science, 359(6377), 725–726. http://dx.doi.org/10.1126/science.359.6377.725.

Katz, D. S., Gruenpeter, M. & Honeyman, T. (2021). Taking a Fresh Look at FAIR for Research Software. Patterns 2, 3. https://doi.org/10.1016/j.patter.2021.100222.

Konkol, M., Kray, C., & Pfeiffer, M. (2018). 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. https://doi.org/10.1080/13658816.2018.1508687.

Konkol, M., Nüst, D. & Goulier, L. (2020). Publishing computational research – a review of infrastructures for reproducible and transparent scholarly communication. Res Integr Peer Rev 5, 10. https://doi.org/10.1186/s41073-020-00095-y.

Krishnamurthi, S. & Vitek, J. (2015). The real software crisis: repeatability as a core value. Commun. ACM 58, 3, 34–36. https://doi.org/10.1145/2658987.

Lasser, J. (2020). Creating an executable paper is a journey through Open Science. Commun Phys 3, 143. https://doi.org/10.1038/s42005-020-00403-4.

Lewis, L.M. et al., 2018. Replication Study: Transcriptional amplification in tumor cells with elevated c-Myc. eLife, 7. <Available at: http://dx.doi.org/10.7554/elife.30274>.

Makowski, D. (2018). How to Cite Packages. R-bloggers. https://www.r-bloggers.com/2018/08/how-to-cite-packages/.

Markowetz, F. (2015). Five selfish reasons to work reproducibly. Genome Biol 16, 274. https://doi.org/10.1186/s13059-015-0850-7.

Marwick, B. (2015). How computers broke science – and what we can do to fix it. The Conversation. https://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938.

McKiernan, E.C. et al. (2016). Author response: How open science helps researchers succeed. http://dx.doi.org/10.7554/elife.16800.008.

Nature Human Behavior. Supporting computational reproducibility through code review. Nat Hum Behav 5, 965–966 (2021). https://doi.org/10.1038/s41562-021-01190-w.

Nüst, D., Ostermann, F. O., Sileryte, R., Hofer, B., Granell, C., Teperek, M., … Wang, Y. (2021). AGILE Reproducible Paper Guidelines. https://doi.org/10.17605/OSF.IO/CB7Z8.

Nüst et al. (2017). Opening the Publication Process with Executable Research Compendia. D-Lib Magazine. http://www.dlib.org/dlib/january17/nuest/01nuest.html.

Nüst, D. & Eglen S. J. CODECHECK: an Open Science initiative for the independent execution of computations underlying research articles during peer review to improve reproducibility. F1000Research 2021, 10:253. https://doi.org/10.12688/f1000research.51738.2.

Open Source Initiative. https://opensource.org/.

Peng, R.D. (2011). Reproducible Research in Computational Science. Science, 334(6060), 1226–1227. http://dx.doi.org/10.1126/science.1213847.

Quintana, D. S. (2020, December 5). Five things about open and reproducible science that every early career researcher should know. https://doi.org/10.17605/OSF.IO/DZTVQ.

RStudio (2020). R Markdown Introduction. URL: https://rmarkdown.rstudio.com/lesson-1.html.

Sandve, G. K., Nekrutenko, A., Taylor, J., Hovig, E. (2013). Ten Simple Rules for Reproducible Computational Research. PLoS Comput Biol 9(10): e1003285. https://doi.org/10.1371/journal.pcbi.1003285.

Stark, P. B. (2018). Before reproducibility must come preproducibility. Nature, 557(7707), 613–613. https://doi.org/10.1038/d41586-018-05256-0.

Stodden, V., McNutt, M., Bailey, D. H., Deelman, E., Gil, Y., Hanson, B., … & Taufer, M. (2016). Enhancing reproducibility for computational methods. Science, 354(6317), 1240–1241. https://doi.org/10.1126/science.aah6168.

The Carpentries (2022). Version Control with Git. https://swcarpentry.github.io/git-novice/index.html.

The Jupyter Book Community. UC Berkeley Data Science Modules. https://ds-modules.github.io/modules-textbook/introduction/ds-intro.html.

The Royal Society. Philosophical Transactions: 350 years of publishing at the Royal Society (1665 – 2015). https://royalsociety.org/-/media/publishing350/publishing350-exhibition-catalogue.pdf.

The Turing Way Community, Arnold, B., Bowler, L., Gibson, S., Herterich, P., Higman, R. … & Whitaker, K. (2019). The Turing Way: A Handbook for Reproducible Data Science. Zenodo. http://doi.org/10.5281/zenodo.3233986

Open Data

Resources on Open Data: Last access of all URLs: 17th November, 2021.

Austin, C. C., Brown, S., Fong, N., Humphrey, C., Leahey, A., & Webster, P. (2016). Research Data Repositories: Review of Current Features, Gap Analysis, and Recommendations for Minimum Requirements. IASSIST Quarterly, 39(4), 24. https://doi.org/10.29173/iq904.

Banda, J. M., Tekumalla, R., Wang, G., Yu, J., Liu, T., Ding, Y., Artemova, K., Tutubalina, E., & Chowell, G. (2021). A large-scale COVID-19 Twitter chatter dataset for open scientific research – an international collaboration [Data set]. Epidemiologia, 2(3). https://doi.org/10.5281/zenodo.5595136.

Berenbaum, M. R. (2021). Editorial Expression of Concern. PNAS, 118(24). https://doi.org/10.1073/pnas.2108930118.

Bill & Melinda Gates Foundation (2021). Open Access Policy. https://openaccess.gatesfoundation.org/open-access-policy/.

Braak, P., Jonge, H., Trentacosti, G., Verhagen, I. & Woutersen-Windhouwer, S. (2020). Guide to Creative Commons for Scholarly Publications and Educational Resources. https://doi.org/10.5281/zenodo.4090923.

Core Trust Seal (2022). https://www.coretrustseal.org/.

DANS (2022). File Formats. https://dans.knaw.nl/en/file-formats/.

DFG (2021). Checklist Regarding the Handling of Research Data. https://www.dfg.de/download/pdf/foerderung/grundlagen_dfg_foerderung/forschungsdaten/forschungsdaten_checkliste_en.pdf.

European Commission. What is open research data? https://ec.europa.eu/info/research-and-innovation/strategy/strategy-2020-2024/our-digital-future/open-science/open-science-monitor/facts-and-figures-open-research-data_en.

European Commission. Open Research Europe – Data Guidelines. https://open-research-europe.ec.europa.eu/for-authors/data-guidelines#opendata.

Science, Digital; Simons, N., Goodey, G., Hardeman, M., Clare, C., Gonzales, S., et al. (2021). The State of Open Data 2021. Digital Science. https://doi.org/10.6084/m9.figshare.17061347.v1.

Funk, C. (2021). Trust and the Science-Policy-Society Interface. Pew Research Center. https://www.un.org/sites/un2.un.org/files/2021/07/funk_-_ppt.pdf.

GitHub. Choose an open source license. https://choosealicense.com/.

Gonzalez-Beltran, A. (2018). Interact to Interoperate. Software Sustainability Institute. https://software.ac.uk/blog/2018-12-06-interact-interoperate.

Higman, R., Bangert, D., & Jones, S. (2019). Three camps, one destination: the intersections of research data management, FAIR and Open. Insights, 32(1). http://doi.org/10.1629/uksg.468.

Hrynaszkiewicz, I. & Cockerill, M. (2012). Open by default: a proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals, BMC Res Notes, 5(494). https://doi.org/10.1186/1756-0500-5-494.

Hufton, A. L. (2022). Dispelling common data sharing myths. https://alhufton.com/dispelling-common-data-sharing-myths/.

Hessels, L. K., Koens, L., & Diederen, P. (2021). Perspectives on the future of Open Science. Effects of global variation in open science practices on the European research system. https://www.doi.org/10.2777/054281.

Labastida, I. & Margoni, T. (2020). Licensing FAIR Data for Reuse. Data Intelligence, 2(1-2). https://doi.org/10.1162/dint_a_00042.

Lin, D., Crabtree, J., Dillo, I. et al. (2020). The TRUST Principles for digital repositories. Scientific Data, 7(144). https://doi.org/10.1038/s41597-020-0486-7.

López de San Román, A. (2021). Recent developments in the EC policy on Open Science. Max Planck Digital Library. https://pure.mpg.de/rest/items/item_3328552_1/component/file_3328558/content.

Miyakawa, T. (2020). No raw data, no science: another possible source of the reproducibility crisis. Molecular Brain, 13(24). https://doi.org/10.1186/s13041-020-0552-2.

Nosek, B. A., Alter, G., Banks, G. C., Borsboom, D., Bowman, S. D., Breckler, S. J., … DeHaven, A. C. (2016). Transparency and Openness Promotion (TOP) Guidelines. Science, 348(6242) https://doi.org/10.1126/science.aab2374.

OpenAIRE (2017). What is open research data? https://www.openaire.eu/what-is-open-research-data.

OpenAIRE. How to find a trustworthy repository for your data. https://www.openaire.eu/find-trustworthy-data-repository.

Open Knowledge Foundation. Open Data Handbook. http://opendatahandbook.org/.

Peiffer-Smadja, N., Maatoug, R., Lescure, FX. et al. (2020). Machine Learning for COVID-19 needs global collaboration and data-sharing. Nature Machine Intelligence, 2(293–294). https://doi.org/10.1038/s42256-020-0181-6

re3data.org. Registry of Research Data Repositories. https://doi.org/10.17616/R3D

Research Data Alliance International Indigenous Data Sovereignty Interest Group (2019). CARE Principles for Indigenous Data Governance. The Global Indigenous Data Alliance. https://www.gida-global.org/care.

Schmidt, B. (2021). Keynote by Brian Schmidt at the Opening Ceremony of #LINO19 – Big Questions for Society, Big Questions for Research. https://www.mediatheque.lindau-nobel.org/videos/38253/keynote-address-brian-schmidt-2019.

Schönbrodt, F. D., Mellor, D. T., Bergmann, C., Penfold, N., Westwood, S. J., Lautarescu, A., … Tananbaum, G. (2021). Academic job offers that mentioned open science. https://doi.org/10.17605/OSF.IO/7JBNT.

Sheehan, J. (2016). Increasing Access to the Results of Federally Funded Science. The White House. https://obamawhitehouse.archives.gov/blog/2016/02/22/increasing-access-results-federally-funded-science.

Theobald, A. Introduction to Creative Commons Licenses. https://uniofcam.libwizard.com/f/CreativeCommons.

Traynor, C., Foster, L., & Schonwetter, T. (2019). Fieldnotes on Tensions Related to Openness in Researching Indigenous Peoples Knowledge Systems and Intellectual Property Rights. Contextualizing Openness. http://hdl.handle.net/2022/24570

UK Research and Innovation (2021). Publishing your research findings. https://www.ukri.org/manage-your-award/publishing-your-research-findings/making-your-research-data-open/.

UNESCO (2021). UNESCO Recommendation on Open Science. https://en.unesco.org/science-sustainable-future/open-science/recommendation.

United Nations, Sustainable Development Goals. https://sdgs.un.org/goals.

University of Cambridge. Research data – Looking after and sharing your data. https://www.data.cam.ac.uk/data-management-guide/looking-after-and-sharing-your-data#Selection.

University of Leeds. Research data management explained – What is research data? https://library.leeds.ac.uk/info/14062/research_data_management/61/research_data_management_explained.

Vines, T. H., Albert, A. Y., Andrew, R. L., Débarre, F., Bock, D. G., Franklin, M. T., … & Rennison, D. J. (2014). The availability of research data declines rapidly with article age. Current biology, 24(1). https://doi.org/10.1016/j.cub.2013.11.014.

Wilkinson, M., Dumontier, M., Aalbersberg, I. et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3, 160018. https://doi.org/10.1038/sdata.2016.18.