Open Science

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.

Academic year 2023/2024

Table of content

• Open Science
  • Academic year 2023/2024
    • Table of content
    • Material
    • Extras
    • Schedule

Material

1. [20/03/24] Introduction to Open Science

   • Introduction to the course: slide
   • Theoretical part: slide
   • Practical part (Project Presentation): slide
   • Bibliography
     • 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
     • Daquino, M., Peroni, S., Shotton, D., Colavizza, G., Ghavimi, B., Lauscher, A., Mayr, P., Romanello, M., & Zumstein, P. (2020). The OpenCitations Data Model. The Semantic Web – ISWC 2020, 12507, 447–463. https://doi.org/10.1007/978-3-030-62466-8_28
     • 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
     • Hendricks, G., Tkaczyk, D., Lin, J., & Feeney, P. (2020). Crossref: The sustainable source of community-owned scholarly metadata. Quantitative Science Studies, 1(1), 414–427. https://doi.org/10.1162/qss_a_00022
     • Imming, M., & Tennant, J. (2018). Sticker open science: Just science done right. https://doi.org/10.5281/ZENODO.1285575
     • International DOI Foundation. (2019). DOI® Handbook. https://doi.org/10.1000/182
     • 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
     • Massari, A., Mariani, F., Heibi, I., Peroni, S., & Shotton, D. (2024). OpenCitations Meta. Quantitative Science Studies. https://doi.org/10.1162/qss_a_00292
     • Peroni, S., & Shotton, D. (2018). Open Citation: Definition. Figshare. https://doi.org/10.6084/m9.figshare.6683855
     • Peroni, S., & Shotton, D. (2020). OpenCitations, an infrastructure organization for open scholarship. Quantitative Science Studies, 1(1), 428–444. https://doi.org/10.1162/qss_a_00023
     • Persiani, S., Daquino, M., & Peroni, S. (2022). A Programming Interface for Creating Data According to the SPAR Ontologies and the OpenCitations Data Model. In P. Groth, M.-E. Vidal, F. Suchanek, P. Szekley, P. Kapanipathi, C. Pesquita, H. Skaf-Molli, & M. Tamper (Eds.), The Semantic Web (Vol. 13261, pp. 305–322). Springer. https://doi.org/10.1007/978-3-031-06981-9_18
     • Reproducibility. (2021). In English Wikipedia. https://en.wikipedia.org/wiki/Reproducibility
     • 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
     • Woelfle, M., Olliaro, P., & Todd, M. H. (2011). Open science is a research accelerator. Nature Chemistry, 3(10), 745–748. https://doi.org/10.1038/nchem.1149

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2. [22/03/24] Reproducibility

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography
     • Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533(7604), 452–454. https://doi.org/10.1038/533452a
     • Barzaghi, S., Bordignon, A., Gualandi, B., & Peroni, S. (2024). Thinking Outside the Black Box: Insights from a Digital Exhibition in the Humanities. https://doi.org/10.48550/arxiv.2402.12000
     • Cobo, M. J., Dehdarirad, T., García-Sánchez, P., & Moral-Munoz, J. A. (2018). Quantifying the reproducibility of scientometric analyses: A case study. STI 2018 Conference Proceedings, 925–933. https://hdl.handle.net/1887/65242
     • 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
     • Heibi, I., & Peroni, S. (2021). A qualitative and quantitative analysis of open citations to retracted articles: The Wakefield et al.’s case. Scientometrics, 126(10), 8433–8470. https://doi.org/10.1007/s11192-021-04097-5
     • Heibi, I., & Peroni, S. (2022). A quantitative and qualitative open citation analysis of retracted articles in the humanities. Quantitative Science Studies, 3(4), 953–975. https://doi.org/10.1162/qss_a_00222
     • 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
     • Moylan, E. C., & Kowalczuk, M. K. (2016). Why articles are retracted: A retrospective cross-sectional study of retraction notices at BioMed Central. BMJ Open, 6(11), e012047. https://doi.org/10.1136/bmjopen-2016-012047
     • Peels, R. (2019). Replicability and replication in the humanities. Research Integrity and Peer Review, 4(1), 2. https://doi.org/10.1186/s41073-018-0060-4
     • Peels, R., & Bouter, L. (2018). The possibility and desirability of replication in the humanities. Palgrave Communications, 4(1), 95. https://doi.org/10.1057/s41599-018-0149-x
     • 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
     • Schnell, S. (2015). Ten Simple Rules for a Computational Biologist’s Laboratory Notebook. PLOS Computational Biology, 11(9), e1004385. https://doi.org/10.1371/journal.pcbi.1004385
     • Velden, T., Hinze, S., Scharnhorst, A., Schneider, J. W., & Waltman. (2018). Exploration of reproducibility issues in scientometric research. In R. Costas, T. Franssen, & A. Yegros-Yegros (Eds.), STI 2018 Conference Proceedings (pp. 612–624). Centre for Science and Technology Studies. https://hdl.handle.net/1887/65315

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3. [27/03/24] FAIR and Open Data

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography
     • 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
     • Belhajjame, K., B’Far, R., Cheney, J., Coppens, S., Cresswell, S., Gil, Y., Groth, P., Klyne, G., Lebo, T., McCusker, J., Miles, S., Myers, J., Sahoo, S., & Tilmes, C. (2013). PROV-DM: The PROV Data Model [W3C Recommendation]. World Wide Web Consortium. https://www.w3.org/TR/prov-dm/
     • 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
     • GO FAIR. (2018). FAIR Principles. https://www.go-fair.org/fair-principles/
     • 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
     • Haak, L. L., Fenner, M., Paglione, L., Pentz, E., & Ratner, H. (2012). ORCID: A system to uniquely identify researchers. Learned Publishing, 25(4), 259–264. https://doi.org/10.1087/20120404
     • 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
     • Lin, D., Crabtree, J., Dillo, I., Downs, R. R., Edmunds, R., Giaretta, D., De Giusti, M., L’Hours, H., Hugo, W., Jenkyns, R., Khodiyar, V., Martone, M. E., Mokrane, M., Navale, V., Petters, J., Sierman, B., Sokolova, D. V., Stockhause, M., & Westbrook, J. (2020). The TRUST Principles for digital repositories. Scientific Data, 7(1), 144. https://doi.org/10.1038/s41597-020-0486-7
     • Michener, W. K. (2015). Ten Simple Rules for Creating a Good Data Management Plan. PLOS Computational Biology, 11(10), e1004525. https://doi.org/10.1371/journal.pcbi.1004525
     • Open Knowledge Foundation. (2015). Open Definition 2.1. https://opendefinition.org/od/2.1/en/
     • Piwowar, H., Priem, J., Larivière, V., Alperin, J. P., Matthias, L., Norlander, B., Farley, A., West, J., & Haustein, S. (2017). Data From: The State Of Oa: A Large-Scale Analysis Of The Prevalence And Impact Of Open Access Articles [dataset]. Zenodo. https://doi.org/10.5281/zenodo.837901
     • 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
     • Wolfe, M. (2017, August 9). CC0 and Data Citation. https://www.library.ucdavis.edu/news/cc0-and-data-citation/

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4. [03/04/24] Open Methodology

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography
     • 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
     • Celebi, R., Rebelo Moreira, J., Hassan, A. A., Ayyar, S., Ridder, L., Kuhn, T., & Dumontier, M. (2020). Towards FAIR protocols and workflows: The OpenPREDICT use case. PeerJ Computer Science, 6, e281. https://doi.org/10.7717/peerj-cs.281
     • 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
     • Goble, C., Cohen-Boulakia, S., Soiland-Reyes, S., Garijo, D., Gil, Y., Crusoe, M. R., Peters, K., & Schober, D. (2020). FAIR Computational Workflows. Data Intelligence, 2(1–2), 108–121. https://doi.org/10.1162/dint_a_00033
     • 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
     • Teytelman, L., Stoliartchouk, A., Kindler, L., & Hurwitz, B. L. (2016). Protocols.io: Virtual Communities for Protocol Development and Discussion. PLOS Biology, 14(8), e1002538. https://doi.org/10.1371/journal.pbio.1002538
     • Watson, M. (2015). When will ‘open science’ become simply ‘science’? Genome Biology, 16(1), 101. https://doi.org/10.1186/s13059-015-0669-2

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5. [05/04/24] Open Peer Review

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography
     • Coalition for Advancing Research Assessment. (2022). Agreement on Reforming Research Assessment [Policy]. European Science Foundation. https://coara.eu/agreement/the-agreement-full-text/
     • Economic and Social Research Council, UKRI. (2019). Data management plan: Guidance for peer reviewers. https://esrc.ukri.org/files/about-us/policies-and-standards/data-management-plan-guidance-for-per-reviewers/
     • 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, available in OA at http://www.semantic-web-journal.net/system/files/swj1301.pdf
     • Janowicz, K., & Hitzler, P. (2012). Open and transparent: The review process of the Semantic Web journal. Learned Publishing, 25(1), 48–55. https://doi.org/10.1087/20120107
     • 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
     • McPeek, M. A., DeAngelis, D. L., Shaw, R. G., Moore, A. J., Rausher, M. D., Strong, D. R., Ellison, A. M., Barrett, L., Rieseberg, L., Breed, M. D., Sullivan, J., Osenberg, C. W., Holyoak, M., & Elgar, M. A. (2009). The Golden Rule of Reviewing. The American Naturalist, 173(5), E155–E158. https://doi.org/10.1086/598847
     • Reviewer’s rights and duties. (2019). https://open-sci.github.io/review/
     • Ross-Hellauer, T. (2017). What is open peer review? A systematic review. F1000Research, 6, 588. https://doi.org/10.12688/f1000research.11369.2
     • Snodgrass, R. T. (2007). Editorial: Single- versus double-blind reviewing. ACM Transactions on Database Systems, 32(1), 1. https://doi.org/10.1145/1206049.1206050
     • Stiller-Reeve, M. (2018). How to write a thorough peer review. Nature. https://doi.org/10.1038/d41586-018-06991-0
     • Tennant, J. P. (2018). The state of the art in peer review. FEMS Microbiology Letters, 365(19). https://doi.org/10.1093/femsle/fny204
     • Tennant, J. P., Crane, H., Crick, et al. (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/
     • Waltman, L., Larivière, V., & Milojević, S. (2022, March 17). Quantitative Science Studies successfully completes transparent peer review pilot [Blog]. ISSI Blog. https://www.issi-society.org/blog/posts/2022/march/quantitative-science-studies-successfully-completes-transparent-peer-review-pilot/

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6. [10/04/24] Open Source Software

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography:
     • 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, available in OA at https://hal.archives-ouvertes.fr/hal-02157125
     • 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, available in OA at https://hal.archives-ouvertes.fr/hal-02135891
     • Chacon, S., & Straub, B. (2014). Pro Git (Second edition). Apress. https://git-scm.com/book/en/v2
     • 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, available in OA at https://arxiv.org/abs/2002.01035
     • Cosmo, R. D., Gruenpeter, M., & Zacchiroli, S. (2020). Referencing Source Code Artifacts: A Separate Concern in Software Citation. Computing in Science & Engineering, 22(2), 33–43. https://doi.org/10.1109/MCSE.2019.2963148, available in OA at https://arxiv.org/abs/2001.08647
     • 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
     • Lamprecht, A.-L., Garcia, L., Kuzak, M., Martinez, C., Arcila, R., Martin Del Pico, E., Dominguez Del Angel, V., van de Sandt, S., Ison, J., Martinez, P. A., McQuilton, P., Valencia, A., Harrow, J., Psomopoulos, F., Gelpi, J. Ll., Chue Hong, N., Goble, C., & Capella-Gutierrez, S. (2020). Towards FAIR principles for research software. Data Science, 3(1), 37–59. https://doi.org/10.3233/DS-190026
     • Martinez-Ortiz, C., Martinez Lavanchy, P., Sesink, L., Olivier, B. G., Meakin, J., de Jong, M., & Cruz, M. (2023). Practical guide to Software Management Plans (Version 1.1). Netherlands eScience Center and NWO. https://doi.org/10.5281/zenodo.7589725
     • Nuvolari, A. (2005). Open source software development: Some historical perspectives. First Monday. https://doi.org/10.5210/fm.v10i10.1284
     • Open Source Initiative. (2007). 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
     • Tennant, J., Agarwal, R., Baždarić, K., Brassard, D., Crick, T., Dunleavy, D. J., Evans, T. R., Gardner, N., Gonzalez-Marquez, M., Graziotin, D., Greshake Tzovaras, B., Gunnarsson, D., Havemann, J., Hosseini, M., Katz, D. S., Knöchelmann, M., Madan, C. R., Manghi, P., Marocchino, A., … Yarkoni, T. (2020). A tale of two ‘opens’: Intersections between Free and Open Source Software and Open Scholarship [Preprint]. SocArXiv. https://doi.org/10.31235/osf.io/2kxq8

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7. [17/04/24] Open Access

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography:
     • 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
     • 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
     • Chan, L., Cuplinskas, D., Eisen, M., Friend, F., Genova, Y., Guédon, J.-C., Hagemann, M., Harnad, S., Johnson, R., Kupryte, R., La Manna, M., Rév, I., Segbert, M., de Souza, S., Suber, P., & Velterop, J. (2002). Read the Budapest Open Access Initiative. https://www.budapestopenaccessinitiative.org/read
     • Cobb, M. (2017). The prehistory of biology preprints: A forgotten experiment from the 1960s. PLOS Biology, 15(11), e2003995. https://doi.org/10.1371/journal.pbio.2003995
     • Else, H. (2021). A guide to Plan S: The open-access initiative shaking up science publishing. Nature, d41586-021-00883–00886. https://doi.org/10.1038/d41586-021-00883-6
     • European Union. (2015). Open access. https://ec.europa.eu/research/participants/docs/h2020-funding-guide/cross-cutting-issues/open-access-data-management/open-access_en.htm
     • 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
     • Kallestinova, E. D. (2011). How to write your first research paper. The Yale Journal of Biology and Medicine, 84(3), 181–190. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178846/
     • 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
     • Redhead, C. (2012, October 23). Why CC-BY? Blog of the Open Access Scholarly Publishing Association. https://oaspa.org/why-cc-by/
     • 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
     • UNESCO. (2013). UNESCO Open Access Publications. https://en.unesco.org/open-access/

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8. [19/04/24] Open Metrics

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography:
     • Artrake Studio. (2020, June). What can DNA test really tell us about our ancestry? https://www.ted.com/talks/prosanta_chakrabarty_what_can_dna_tests_really_tell_us_about_our_ancestry
     • Baccini, A., De Nicolao, G., & Petrovich, E. (2019). Citation gaming induced by bibliometric evaluation: A country-level comparative analysis. PLOS ONE, 14(9), e0221212. https://doi.org/10.1371/journal.pone.0221212
     • Cagan, R. (2013). The San Francisco Declaration on Research Assessment. Disease Models & Mechanisms, 6(4), 869–870. https://doi.org/10.1242/dmm.012955
     • Cameron, R. D. (1997). A Universal Citation Database As a Catalyst For Reform In Scholarly Communication. First Monday, 2(4). https://doi.org/10.5210/fm.v2i4.522
     • Else, H. (2018). How Unpaywall is transforming open science. Nature, 560(7718), 290–291. https://doi.org/10.1038/d41586-018-05968-3
     • 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, available in OA at http://garfield.library.upenn.edu/essays/v6p468y1983.pdf)
     • 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, available in OA at https://garfield.library.upenn.edu/papers/jamajif2006.pdf)
     • Haak, L. L., Fenner, M., Paglione, L., Pentz, E., & Ratner, H. (2012). ORCID: A system to uniquely identify researchers. Learned Publishing, 25(4), 259–264. https://doi.org/10.1087/20120404
     • Hendricks, G., Kramer, B., Maccallum, C., Manghi, P., Neylon, C., Peroni, S., Shotton, D., Tay, A., & Waltman, L. (2021, ottobre 27). Now is the time to work together toward open infrastructures for scholarly metadata. [Blog]. LSE Impact Blog. https://blogs.lse.ac.uk/impactofsocialsciences/2021/10/27/now-is-the-time-to-work-together-toward-open-infrastructures-for-scholarly-metadata/
     • Hicks, D., Wouters, P., Waltman, L., de Rijcke, S., & Rafols, I. (2015). Bibliometrics: The Leiden Manifesto for research metrics. Nature, 520(7548), 429–431. https://doi.org/10.1038/520429a
     • 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
     • Larivière, V., & Sugimoto, C. R. (2019). The Journal Impact Factor: A Brief History, Critique, and Discussion of Adverse Effects. In W. Glänzel, H. F. Moed, U. Schmoch, & M. Thelwall (Eds.), Springer Handbook of Science and Technology Indicators (pp. 3–24). Springer International Publishing. https://doi.org/10.1007/978-3-030-02511-3_1, availablie in OA at https://arxiv.org/abs/1801.08992
     • Mohammadi, E., Thelwall, M., Kwasny, M., & Holmes, K. L. (2018). Academic information on Twitter: A user survey. PLOS ONE, 13(5), e0197265. https://doi.org/10.1371/journal.pone.0197265
     • Priem, J., Groth, P., & Taraborelli, D. (2012). The Altmetrics Collection. PLoS ONE, 7(11), e48753. https://doi.org/10.1371/journal.pone.0048753
     • Rettberg, N., & Schmidt, B. (2012). OpenAIRE - Building a collaborative Open Access infrastructure for European researchers. LIBER Quarterly, 22(3), 160. https://doi.org/10.18352/lq.8110
     • 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
     • Visser, M., van Eck, N. J., & Waltman, L. (2021). Large-scale comparison of bibliographic data sources: Scopus, Web of Science, Dimensions, Crossref, and Microsoft Academic. Quantitative Science Studies, 2(1), 20–41. https://doi.org/10.1162/qss_a_00112
     • 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
     • Wang, K., Shen, Z., Huang, C., Wu, C.-H., Dong, Y., & Kanakia, A. (2020). Microsoft Academic Graph: When experts are not enough. Quantitative Science Studies, 1(1), 396–413. https://doi.org/10.1162/qss_a_00021

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9. [24/04/24] Open Infrastructures

   • Theoretical part: slide
   • Practical part: slide
   • Bibliography:
     • Alexandrov, A. V., & Hennerici, M. G. (2013). How to Prepare and Deliver a Scientific Presentation. Cerebrovascular Diseases, 35(3), 202–208. https://doi.org/10.1159/000346077
     • Allen, L., O’Connell, A., & Kiermer, V. (2019). How can we ensure visibility and diversity in research contributions? How the Contributor Role Taxonomy (CRediT) is helping the shift from authorship to contributorship. Learned Publishing, 32(1), 71–74. https://doi.org/10.1002/leap.1210
     • Aspesi, C., & Brand, A. (2020). In pursuit of open science, open access is not enough. Science, 368(6491), 574–577. https://doi.org/10.1126/science.aba3763
     • Bilder, G., Lin, J., & Neylon, C. (2020). The Principles of Open Scholarly Infrastructure. The Principles of Open Scholarly Infrastructure. https://doi.org/10.24343/C34W2H
     • Burgelman, J.-C. (2021). Politics and Open Science: How the European Open Science Cloud Became Reality (the Untold Story). Data Intelligence, 3(1), 5–19. https://doi.org/10.1162/dint_a_00069
     • Doumont, J. (2011). Creating Effective Presentation Slides. Optics & Photonics News, 22(3), 12–14. https://www.osa-opn.org/home/articles/volume_22/issue_3/departments/career_focus/creating_effective_presentation_slides/
     • European Strategy Forum on Research Infrastructures. (2021). Roadmap 2021: Strategy Report on Research Infrastructures. Università degli Studi di Milano. https://roadmap2021.esfri.eu/
     • 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
     • 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
     • 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/
     • Skinner, K., & Lippincott, S. (2020). Assessment Checklist (Commonplace). Knowledge Futures Group. https://doi.org/10.21428/6ffd8432.5175bab1/00710d8a
     • 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/

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10. [08/05/24] Final seminar

    • Title: Open science: in dialogue with society
    • Abstract: We shall explore the two-way connection among science and society - as Open Science is not just "sharing" at the end of the process, it's a different way of creating knowledge starting from the beginning, and possibly co-creating it. After discussing the potentiality of citizen science, we shall delve into the realm of science communication with a focus on science for policy, for a truly evidence-informed policy making.
    • Speaker: Elena Giglia, PhD, Masters' Degree in Librarianship and Masters' Degree in Public Institutions Management, is Head of the Open Science Unit at the University of Turin. She has been part of the European Open Science network for many years, attending national and international conferences, and writing and lecturing on Open Access and Open Science. She was a member (2019-2020) of the Committee on Open Science at the Ministry for University and Research (MUR). She actively collaborates with the ICDI – Italian Computer and Data Infrastructure Competence center on Open Science, EOSC and FAIR data and with several national and international projects. She represents OPERAS Research Infrastructure in the EOSC Association. She serves in several Scientific Committees and Advisory Boards.

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11. [27 May 2024, 10:00-13:00] Workshop

    • 10:00-10:15: welcoming and instructions
    • 10:15-10:30: presentation of the invited experts
    • 10:30-11:30: project presentation by Harkonnen
    • 11:30-11:45: break
    • 11:45-12:45: project presentation by Atreides

Extras

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

Schedule

20/03/24	12:00-15:00	Introduction to Open Science
22/03/24	12:00-15:00	Reproducibility
27/03/24	12:00-15:00	FAIR and Open Data
03/04/24	12:00-15:00	Open Methodology
05/04/24	12:00-15:00	Open Peer Review
10/04/24	12:00-15:00	Open Source Software
17/04/24	12:00-15:00	Open Access
19/04/24	12:00-15:00	Open Metrics
24/04/24	12:00-15:00	Open Infrastructures
08/05/24	12:00-15:00	Final seminar