Skip to content

The GitHub repository containing all the material related to the Open Science course of the Digital Humanities and Digital Knowledge degree at the University of Bologna (a.a. 2024/2025).

Notifications You must be signed in to change notification settings

open-sci/2024-2025

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

36 Commits
 
 
 
 
 
 
 
 

Repository files navigation

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 2024/2025

Table of content

Material

  1. [31/3/25] Introduction to Open Science


  2. [3/4/25] Reproducibility


  3. [7/4/25] FAIR and Open Data

    • Mandatory reading (to read and study before the lecture):
      • Carroll, S. R., Garba, I., Figueroa-Rodríguez, O. L., Holbrook, J., Lovett, R., Materechera, S., Parsons, M., Raseroka, K., Rodriguez-Lonebear, D., Rowe, R., Sara, R., Walker, J. D., Anderson, J., & Hudson, M. (2020). The CARE Principles for Indigenous Data Governance. Data Science Journal, 19, 43. https://doi.org/10.5334/dsj-2020-043
    • 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

  4. [10/4/25] Open Methodology

    • Mandatory reading (to read and study before the lecture):
    • 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

  5. [14/4/25] Open Peer Review


  6. [28/4/25] Open Source Software

    • Mandatory reading (to read and study before the lecture):
      • Borisova, E., Abu Ahmad, R., Garcia-Castro, L., Usbeck, R., & Rehm, G. (2024). Surveying the FAIRness of Annotation Tools: Difficult to find, difficult to reuse. Proceedings of The 18th Linguistic Annotation Workshop (LAW-XVIII), 29–45. https://aclanthology.org/2024.law-1.4/
    • Theoretical part: slide
    • Supplementary bibliography (optional):

  7. [5/5/25] Open Access


  8. [8/5/25] Open Metrics


  9. [12/5/25] Open Infrastructures


  10. [15/5/25] Wrap-up session


  11. [27/6/25] Workshop

Extras

Video presentations about Open Science stuff:

Schedule

31/3/2513:00-16:00Introduction to Open Science
3/4/2512:00-15:00Reproducibility
7/4/2513:00-16:00FAIR and Open Data
10/4/2512:00-15:00Open Methodology
14/4/2513:00-16:00Open Peer Review
28/4/2513:00-16:00Open Source Software
5/5/2513:00-16:00Open Access
8/5/2512:00-15:00Open Metrics
12/5/2513:00-16:00Open Infrastructures
15/5/2512:00-15:00Wrap-up session

About

The GitHub repository containing all the material related to the Open Science course of the Digital Humanities and Digital Knowledge degree at the University of Bologna (a.a. 2024/2025).

Resources

Stars

Watchers

Forks

Packages

No packages published

Contributors 6