This space contains all the material related to the Open Science course of the Digital Humanities and Digital Knowledge degree at the University of Bologna.
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[9/4/26] Introduction to Open Science
- Introduction to the course: slide
- Theoretical part: slide
- Project Presentation: slide
- Supplementary bibliography (optional):
- Bahlai, C., Bartlett, L., Burgio, K., Fournier, A., Keiser, C., Poisot, T., & Whitney, K. (2019). Open Science Isn’t Always Open to All Scientists. American Scientist, 107(2), 78. https://doi.org/10.1511/2019.107.2.78
- Fecher, B., & Friesike, S. (2014). Open Science: One Term, Five Schools of Thought. In S. Bartling & S. Friesike (Eds.), Opening Science (pp. 17–47). Springer International Publishing. https://doi.org/10.1007/978-3-319-00026-8_2
- Imming, M., & Tennant, J. (2018). Sticker open science: Just science done right [Graphic]. https://doi.org/10.5281/ZENODO.1285575
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Leonelli, S. (2023). Philosophy of Open Science (1st ed.). Cambridge University Press. https://doi.org/10.1017/9781009416368
- Reproducibility. (2025). In English Wikipedia. https://en.wikipedia.org/wiki/Reproducibility
- UNESCO. (2018). Recommendation on Science and Scientific Researchers (Programme and Meeting Document SHS/BIO/PI/2017/3 Rev; p. 24). https://unesdoc.unesco.org/ark:/48223/pf0000263618
- UNESCO. (2021). UNESCO Recommendation on Open Science (Programme and Meeting Document SC-PCB-SPP/2021/OS/UROS; p. 36). https://unesdoc.unesco.org/ark:/48223/pf0000379949
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[13/4/26] Reproducibility
- Mandatory reading (to read and study before the lecture):
- Barzaghi, S., Bordignon, A., Gualandi, B., & Peroni, S. (2025). Enlightening the Black Box of Humanities Research. Methodological Documentation as a Way to Transparency and Accountability of Digital Exhibitions. Umanistica Digitale, 9(20), 97–114. https://doi.org/10.6092/issn.2532-8816/21177
- Theoretical part: slide
- Supplementary bibliography (optional):
- Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533(7604), 452–454. https://doi.org/10.1038/533452a
- European Commission, Directorate General for Research and Innovation, Baker, L., Cristea, I. A., Errington, T. M., Jaśko, K., Lusoli, W., MacCallum, C. J., Parry, V., Pérignon, C., Šimko, T., & Winchester, C. (2020). Reproducibility of scientific results in the EU: Scoping report (W. Lusoli, Ed.). Publications Office. https://doi.org/10.2777/341654
- Fanelli, D. (2018). Opinion: Is science really facing a reproducibility crisis, and do we need it to? Proceedings of the National Academy of Sciences, 115(11), 2628–2631. https://doi.org/10.1073/pnas.1708272114
- Goodman, S. N., Fanelli, D., & Ioannidis, J. P. A. (2016). What does research reproducibility mean? Science Translational Medicine, 8(341). https://doi.org/10.1126/scitranslmed.aaf5027 (OA at https://osf.io/dw23g)
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Peng, R. (2015). The reproducibility crisis in science: A statistical counterattack. Significance, 12(3), 30–32. https://doi.org/10.1111/j.1740-9713.2015.00827.x
- UNESCO. (2021). UNESCO Recommendation on Open Science (Programme and Meeting Document SC-PCB-SPP/2021/OS/UROS; p. 36). https://unesdoc.unesco.org/ark:/48223/pf0000379949
- Mandatory reading (to read and study before the lecture):
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[16/4/26] FAIR and Open Data
- Mandatory reading (to read and study before the lecture):
- Di Donato, F., & Provost, L. (2025). Why isn’t FAIR enough? Bringing together methods and values for Open Science uptake. Umanistica Digitale, 9(19), 17–46. https://doi.org/10.6092/issn.2532-8816/20976
- Theoretical part: slide
- Supplementary bibliography (optional):
- Avanço, K., Balula, A., Błaszczyńska, M., Buchner, A., Caliman, L., Clivaz, C., Costa, C., Franczak, M., Gatti, R., Giglia, E., Gingold, A., Jarmelo, S., Padez, M. J., Leão, D., Maryl, M., Melinščak Zlodi, I., Mojsak, K., Morka, A., Mosterd, T., … Wieneke, L. (2021). Future of Scholarly Communication—Forging an inclusive and innovative research infrastructure for scholarly communication in Social Sciences and Humanities (p. 46). Digital Humanities Centre at the Institute of Literary Research of the Polish Academy of Sciences. https://doi.org/10.5281/zenodo.5017705
- Caldoni, G., Gualandi, B., & Marino, M. (2022). Research Data Management: Decision Tree [Decision tree]. Alma Mater Studiorum - Università di Bologna. https://doi.org/10.5281/zenodo.7190005
- Chue Hong, N. P., Katz, D. S., Barker, M., Lamprecht, A.-L., Martinez, C., Psomopoulos, F. E., Harrow, J., Castro, L. J., Gruenpeter, M., Martinez, P. A., & Honeyman, T. (2022). FAIR Principles for Research Software (FAIR4RS Principles) [RDA Recommendation]. Research Data Alliance. https://doi.org/10.15497/RDA00068
- Gomes, D. G. E., Pottier, P., Crystal-Ornelas, R., Hudgins, E. J., Foroughirad, V., Sánchez-Reyes, L. L., Turba, R., Martinez, P. A., Moreau, D., Bertram, M. G., Smout, C. A., & Gaynor, K. M. (2022). Why don’t we share data and code? Perceived barriers and benefits to public archiving practices. Proceedings of the Royal Society B: Biological Sciences, 289(1987), 20221113. https://doi.org/10.1098/rspb.2022.1113
- Gualandi, B., Caldoni, G., & Marino, M. (2022). Research Data Management: Data Lifecycle [Diagram]. Alma Mater Studiorum - Università di Bologna. https://doi.org/10.5281/zenodo.7249051
- Gualandi, B., Pareschi, L., & Peroni, S. (2022). What do we mean by ‘data’? A proposed classification of data types in the arts and humanities. Journal of Documentation, 79(7), 51–71. https://doi.org/10.1108/JD-07-2022-0146
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Landi, A., Thompson, M., Giannuzzi, V., Bonifazi, F., Labastida, I., da Silva Santos, L. O. B., & Roos, M. (2020). The “A” of FAIR – As Open as Possible, as Closed as Necessary. Data Intelligence, 2(1–2), 47–55. https://doi.org/10.1162/dint_a_00027
- Open Knowledge Foundation. (2015, November). Open Definition 2.1. https://opendefinition.org/od/2.1/en/
- Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 on the Protection of Natural Persons with Regard to the Processing of Personal Data and on the Free Movement of Such Data, and Repealing Directive 95/46/EC (General Data Protection Regulation), L119, Official Journal of the European Union (2016). http://data.europa.eu/eli/reg/2016/679/oj
- Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J.-W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., … Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3, 160018. https://doi.org/10.1038/sdata.2016.18
- Mandatory reading (to read and study before the lecture):
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[20/4/26] Open Methodology
- Mandatory reading (to read and study before the lecture):
- Leonelli, S. (2025). Environmental Intelligence: Redefining the Philosophical Premises of AI. Harvard Data Science Review, 7(4). https://doi.org/10.1162/99608f92.ac7c1504
- Theoretical part: slide
- Supplementary bibliography (optional):
- Beg, M., Taka, J., Kluyver, T., Konovalov, A., Ragan-Kelley, M., Thiery, N. M., & Fangohr, H. (2021). Using Jupyter for Reproducible Scientific Workflows. Computing in Science & Engineering, 23(2), 36–46. https://doi.org/10.1109/MCSE.2021.3052101
- Belhajjame, K., Zhao, J., Garijo, D., Gamble, M., Hettne, K., Palma, R., Mina, E., Corcho, O., Gómez-Pérez, J. M., Bechhofer, S., Klyne, G., & Goble, C. (2015). Using a suite of ontologies for preserving workflow-centric research objects. Journal of Web Semantics, 32, 16–42. https://doi.org/10.1016/j.websem.2015.01.003
- Bolderston, A. (2008). Writing an Effective Literature Review. Journal of Medical Imaging and Radiation Sciences, 39(2), 86–92. https://doi.org/10.1016/j.jmir.2008.04.009
- Clarke, P., Buckell, J., & Barnett, A. (2020). Registered Reports: Time to Radically Rethink Peer Review in Health Economics. PharmacoEconomics - Open, 4(1), 1–4. https://doi.org/10.1007/s41669-019-00190-x
- Crusoe, M. R., Abeln, S., Iosup, A., Amstutz, P., Chilton, J., Tijanić, N., Ménager, H., Soiland-Reyes, S., Gavrilović, B., Goble, C., & Community, T. C. (2022). Methods included: Standardizing computational reuse and portability with the Common Workflow Language. Communications of the ACM, 65(6), 54–63. https://doi.org/10.1145/3486897
- Hrynaszkiewicz, I. (2020, December 7). Show your work. Peer-Reviewed Protocols. The Official PLOS Blog. https://theplosblog.plos.org/2020/12/show-your-work-peer-reviewed-protocols/
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Perneger, T. V. (2004). Writing a research article: Advice to beginners. International Journal for Quality in Health Care, 16(3), 191–192. https://doi.org/10.1093/intqhc/mzh053
- Watson, M. (2015). When will ‘open science’ become simply ‘science’? Genome Biology, 16(1), 101. https://doi.org/10.1186/s13059-015-0669-2
- Mandatory reading (to read and study before the lecture):
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[23/4/26] Open Peer Review
- Mandatory reading (to read and study before the lecture):
- TBD
- Theoretical part: slide
- Supplementary bibliography (optional):
- Coalition for Advancing Research Assessment. (2022). Agreement on Reforming Research Assessment [Policy]. European Science Foundation. https://coara.eu/agreement/the-agreement-full-text/
- Eve, M. P., Neylon, C., O’Donnell, D. P., Moore, S., Gadie, R., Odeniyi, V., & Parvin, S. (2020). Reading Peer Review (1st ed.). Cambridge University Press. https://doi.org/10.1017/9781108783521
- Gangemi, A., Peroni, S., Shotton, D. M., & Vitali, F. (2017). The Publishing Workflow Ontology (PWO). Semantic Web, 8(5), 703–718. https://doi.org/10.3233/SW-160230
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Ross-Hellauer, T. (2017). What is open peer review? A systematic review. F1000Research, 6, 588. https://doi.org/10.12688/f1000research.11369.2
- Tennant, J. P., Crane, H., Crick, T., Davila, J., Enkhbayar, A., Havemann, J., Kramer, B., Martin, R., Masuzzo, P., Nobes, A., Rice, C., Rivera-López, B., Ross-Hellauer, T., Sattler, S., Thacker, P. D., & Vanholsbeeck, M. (2019). Ten Hot Topics around Scholarly Publishing. Publications, 7(2), 34. https://doi.org/10.3390/publications7020034
- Tennant, J. P., Dugan, J. M., Graziotin, D., Jacques, D. C., Waldner, F., Mietchen, D., Elkhatib, Y., B. Collister, L., Pikas, C. K., Crick, T., Masuzzo, P., Caravaggi, A., Berg, D. R., Niemeyer, K. E., Ross-Hellauer, T., Mannheimer, S., Rigling, L., Katz, D. S., Greshake Tzovaras, B., … Colomb, J. (2017). A multi-disciplinary perspective on emergent and future innovations in peer review. F1000Research, 6, 1151. https://doi.org/10.12688/f1000research.12037.3
- UNESCO. (2021). UNESCO Recommendation on Open Science (Programme and Meeting Document SC-PCB-SPP/2021/OS/UROS; p. 36). https://unesdoc.unesco.org/ark:/48223/pf0000379949
- Waltman, L., & Polka, J. (2022, July 7). Making sense of preprints by adding context – The Publish Your Reviews initiative [Blog]. LSE Impact Blog. https://blogs.lse.ac.uk/impactofsocialsciences/2022/07/07/making-sense-of-preprints-by-adding-context-the-publish-your-reviews-initiative/
- Mandatory reading (to read and study before the lecture):
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[27/4/26] Open Source Software
- Mandatory reading (to read and study before the lecture):
- TBD
- Theoretical part: slide
- Supplementary bibliography (optional):
- Abramatic, J.-F., Di Cosmo, R., & Zacchiroli, S. (2018). Building the universal archive of source code. Communications of the ACM, 61(10), 29–31. https://doi.org/10.1145/3183558
- Alliez, P., Cosmo, R. D., Guedj, B., Girault, A., Hacid, M.-S., Legrand, A., & Rougier, N. (2020). Attributing and Referencing (Research) Software: Best Practices and Outlook From Inria. Computing in Science & Engineering, 22(1), 39–52. https://doi.org/10.1109/MCSE.2019.2949413
- Cohen, J., Katz, D. S., Barker, M., Chue Hong, N., Haines, R., & Jay, C. (2021). The Four Pillars of Research Software Engineering. IEEE Software, 38(1), 97–105. https://doi.org/10.1109/MS.2020.2973362
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Nuvolari, A. (2005). Open source software development: Some historical perspectives. First Monday. https://doi.org/10.5210/fm.v10i10.1284
- Open Source Initiative. (2007, March 22). The Open Source Definition. https://opensource.org/osd
- Prlić, A., & Procter, J. B. (2012). Ten Simple Rules for the Open Development of Scientific Software. PLoS Computational Biology, 8(12), e1002802. https://doi.org/10.1371/journal.pcbi.1002802
- Raymond, E. S. (2000). The cathedral and the bazaar: Musings on Linux and open source by an accidental revolutionary (Version 3.0). O’Reilly Media. http://www.catb.org/~esr/writings/cathedral-bazaar/cathedral-bazaar/
- Smith, A. M., Katz, D. S., Niemeyer, K. E., & FORCE11 Software Citation Working Group. (2016). Software citation principles. PeerJ Computer Science, 2, e86. https://doi.org/10.7717/peerj-cs.86
- Mandatory reading (to read and study before the lecture):
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[30/4/26] Open Access
- Mandatory reading (to read and study before the lecture):
- TBD
- Theoretical part: slide
- Supplementary bibliography (optional):
- Bosman, J., Frantsvåg, J. E., Kramer, B., Langlais, P.-C., & Proudman, V. (2021). OA Diamond Journals Study. Part 1: Findings. Zenodo. https://doi.org/10.5281/ZENODO.4558704
- Brainard, J. (2021). Open access takes flight. Science, 371(6524), 16–20. https://doi.org/10.1126/science.371.6524.16
- Fyfe, A. (2021). Self-help for learned journals: Scientific societies and the commerce of publishing in the 1950s. History of Science, 007327532199990. https://doi.org/10.1177/0073275321999901
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Logan, C. J. (2017). We can shift academic culture through publishing choices. F1000Research, 6, 518. https://doi.org/10.12688/f1000research.11415.2
- Piwowar, H., Priem, J., Larivière, V., Alperin, J. P., Matthias, L., Norlander, B., Farley, A., West, J., & Haustein, S. (2018). The state of OA: A large-scale analysis of the prevalence and impact of Open Access articles. PeerJ, 6, e4375. https://doi.org/10.7717/peerj.4375
- Tennant, J. (2018). What do penguins, Gimli, and cobras have to do with Open Science? DARIAH Annual Event 2018, Paris, France. figshare. https://doi.org/10.6084/M9.FIGSHARE.6326339.V1
- Tennant, J. P., Crane, H., Crick, T., Davila, J., Enkhbayar, A., Havemann, J., Kramer, B., Martin, R., Masuzzo, P., Nobes, A., Rice, C., Rivera-López, B., Ross-Hellauer, T., Sattler, S., Thacker, P. D., & Vanholsbeeck, M. (2019). Ten Hot Topics around Scholarly Publishing. Publications, 7(2), 34. https://doi.org/10.3390/publications7020034
- Tennant, J. P., Waldner, F., Jacques, D. C., Masuzzo, P., Collister, L. B., & Hartgerink, Chris. H. J. (2016). The academic, economic and societal impacts of Open Access: An evidence-based review. F1000Research, 5, 632. https://doi.org/10.12688/f1000research.8460.3
- Mandatory reading (to read and study before the lecture):
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[4/5/26] Open Metrics
- Mandatory reading (to read and study before the lecture):
- TBD
- Theoretical part: slide
- Supplementary bibliography (optional):
- Artrake Studio (Director). (2020, June). What can DNA test really tell us about our ancestry? [Video recording]. https://www.ted.com/talks/prosanta_chakrabarty_what_can_dna_tests_really_tell_us_about_our_ancestry
- Barcelona Declaration on Open Research Information. (2024). [Policy]. https://barcelona-declaration.org/
- Cameron, R. D. (1997). A Universal Citation Database. First Monday, 2(4). https://doi.org/10.5210/fm.v2i4.522
- Coalition for Advancing Research Assessment. (2022). Agreement on Reforming Research Assessment [Policy]. European Science Foundation. https://coara.eu/agreement/the-agreement-full-text/
- Garfield, E. (1955). Citation Indexes for Science: A New Dimension in Documentation through Association of Ideas. Science, 122(3159), 108–111. https://doi.org/10.1126/science.122.3159.108
- Garfield, E. (2006). The History and Meaning of the Journal Impact Factor. JAMA, 295(1), 90. https://doi.org/10.1001/jama.295.1.90
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Tennant, J. P., Crane, H., Crick, T., Davila, J., Enkhbayar, A., Havemann, J., Kramer, B., Martin, R., Masuzzo, P., Nobes, A., Rice, C., Rivera-López, B., Ross-Hellauer, T., Sattler, S., Thacker, P. D., & Vanholsbeeck, M. (2019). Ten Hot Topics around Scholarly Publishing. Publications, 7(2), 34. https://doi.org/10.3390/publications7020034
- Waltman, L. (2020, September 9). Responsible research assessment requires open scholarly metadata. Workshop on Open Citations and Open Scholarly Metadata 2020, Bologna, Italy. Zenodo. https://doi.org/10.5281/zenodo.4021492
- Mandatory reading (to read and study before the lecture):
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[7/5/26] Open Infrastructures
- Mandatory reading (to read and study before the lecture):
- TBD
- Theoretical part: slide
- Supplementary bibliography (optional):
- Bilder, G., Lin, J., & Neylon, C. (2023, November). The Principles of Open Scholarly Infrastructure. The Principles of Open Scholarly Infrastructure. https://doi.org/10.24343/C34W2H
- EOSC Association. (2025). EOSC Federation Handbook (Handbook Version 1). EOSC Association. https://doi.org/10.5281/zenodo.14999577
- Ficarra, V., Fosci, M., Chiarelli, A., Kramer, B., & Proudman, V. (2020). Scoping the Open Science Infrastructure Landscape in Europe. SPARC Europe. https://doi.org/10.5281/zenodo.4159838
- Janssen, R., Gramsbergen, E., de Smaele, M., Teperek, M., & Popescu, I. (2023, January 30). We are going free and open source! [Blog]. 4TU.ResearchData Community. https://community.data.4tu.nl/2023/01/30/we-are-going-free-and-open-source/
- Kramer, B., & Bosman, J. (2015, June 18). The good, the efficient and the open—Changing research workflows and the need to move from Open Access to Open Science. CERN Workshop on Innovations in Scholarly Communication (OAI9), University of Geneva, Geneva, Switzerland. https://www.slideshare.net/bmkramer/the-good-the-efficient-and-the-open-oai9
- Teal, T., Lowenberg, D., Smith, T., Gonzales, J. B., Nielsen, L. H., & Ioannidis, A. (2020, August 26). Sustainable, Open Source Alternatives Exist [Blog]. Dryad News and Views. https://blog.datadryad.org/2020/08/26/sustainable-infrastructure-exists/
- Teperek, M., & Dunning, A. (2020, August 18). Why figshare? Choosing a new technical infrastructure for 4TU.ResearchData [Blog]. Open Working. https://openworking.wordpress.com/2020/08/18/why-figshare-choosing-a-new-technical-infrastructure-for-4tu-researchdata/
- Mandatory reading (to read and study before the lecture):
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[14/5/26] Wrap-up session
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[XX/6/26] Workshop
Video presentations about Open Science stuff:
- Tennant, J. (2018, May 23). Open Science is just good science. https://www.youtube.com/watch?v=UEEcwRUgQu8
- Suber, P. (2021, April 14). Let’s talk about...Open Science Infrastructure with Peter Suber (A. Morka, Interviewer) [Youtube]. https://www.youtube.com/watch?v=GwSoFKFCjic
- Thaney, K. (2021, April 23). Let’s talk about... Open Science Infrastructure with Kaitlin Thaney (A. Morka, Interviewer) [Youtube]. https://www.youtube.com/watch?v=kFk2hbtwmqU
| 9/4/26 | 12:00-15:00 | Introduction to Open Science |
| 13/4/26 | 13:00-16:00 | Reproducibility |
| 16/4/26 | 12:00-15:00 | FAIR and Open Data |
| 20/4/26 | 13:00-16:00 | Open Methodology |
| 23/4/26 | 12:00-15:00 | Open Peer Review |
| 27/4/26 | 13:00-16:00 | Open Source Software |
| 30/4/26 | 12:00-15:00 | Open Access |
| 4/5/26 | 13:00-16:00 | Open Metrics |
| 7/5/26 | 12:00-15:00 | Open Infrastructures |
| 14/5/26 | 13:00-16:00 | Wrap-up session |
| xx/6/26 | XXX | Workshop |