Training materials

All slides are available on Zenodo under community ELIXIR-Estonia. Programming code is available on ELIXIR Estonia GitHub page.

Bioinformatics

• Pilvar, D. (2024, November 20). Prompting 101 - A Beginner’s Guide to Communicating with LLMs. Zenodo. https://doi.org/10.5281/zenodo.14190264
• Kolberg, L., & Raudvere, U. (2024, June 3). Introduction to g:Profiler. Zenodo. https://doi.org/10.5281/zenodo.11207911.
• ELIXIR Estonia (2024). R basic https://github.com/ELIXIREstonia/2024-10-02-R-basic
• ELIXIR Estonia (2024). Shell Novice https://github.com/ELIXIREstonia/2024-10-23-shell-novice
• ELIXIR Estonia (2024). Python for Beginners https://github.com/ELIXIREstonia/2024-02-23-Python
• Kerimov, Nurlan (2024). Introduction to Bioinformatics workflows with Nextflow and nf-core https://kerimoff.github.io/workflows-nextflow/index.html
• Adler, P. (2024, November 6). Version Control with Git. https://elixirestonia.github.io/2024-11-06-git/

Data Visualisation

• Pilvar, D. (2024, October 4). Data Visualisation. Zenodo. https://doi.org/10.5281/zenodo.7819286.
• Pilvar, D. (2024, April 12). Tableau for beginners. Zenodo. https://doi.org/10.5281/zenodo.10963883.
• ELIXIR Estonia (2024). R visualisation https://github.com/ELIXIREstonia/2024-10-09-R-visualisation
• Heleri Inno. (2022, October 26). Data Visualisation I - Figures. Zenodo. https://doi.org/10.5281/zenodo.7251489

Useful sites:

• What kind of data do you have? Let the decision tree guide you toward your graphic possibilities.
• C. Li. (2023). cxli233/FriendsDontLetFriends: FriendsDontLetFriends (v3) (Version v3). Zenodo. https://doi.org/10.5281/zenodo.7542491 and https://github.com/cxli233/FriendsDontLetFriends. This is an opinionated essay about good and bad practices in data visualization with examples and explanations
• General considerations for visualising data with examples from infectious disease
• Choosing color palettes https://coolors.co/
• Website to simulate for you what your chosen color palette looks like to viewers who are colorblind.

Collaborations

• Rekand, I., & Conzett, P. (2024, April 8). DataverseNO - A Norwegian, national repository for sharing open and FAIR data. Zenodo. https://doi.org/10.5281/zenodo.10940043.
• Conzett, P., & Rekand, I. (2024, April 5). Data Curation with Dataverse: A Norwegian Perspective. Zenodo. https://doi.org/10.5281/zenodo.10933004.
• Arust, E., Kirss, J., Seppet, L., & Oopkaup, O. E. (2023, March 27). Repositories and HPCs in Estonia. Zenodo. https://doi.org/10.5281/zenodo.8058669
• Tarkpea, T., & Pagan, H. C. (2023, February 28). Open Science and DMP in Estonia + QA by Grant Office. Zenodo. https://doi.org/10.5281/zenodo.7684492

Data Management

• Inno, H. (2024, October 31). Laboratory documentation with Markdown. Zenodo. https://doi.org/10.5281/zenodo.14016131
• Pilvar, D. (2024, September 24). How to make your messy data usable? / OpenRefine. Zenodo. https://doi.org/10.5281/zenodo.13832071
• Pilvar, D. (2024, September 20). Crash Course in Data Management. Zenodo. https://doi.org/10.5281/zenodo.13801447
• Pilvar, D. (2024, May 14). Metadata and README. Zenodo. https://doi.org/10.5281/zenodo.7835048.
• Pilvar, D. (2024, May 1). FAIR in a Nutshell. Zenodo. https://doi.org/10.5281/zenodo.7660007.
• Pilvar, D. (2024, March 1). Bring Your Own Data Management Plan. Zenodo. https://doi.org/10.5281/zenodo.7707813.
• Pilvar, D. (2024, February 23). Andmehaldus 101. Zenodo. https://doi.org/10.5281/zenodo.10006022
• Pilvar, D. (2023, September 5). AKKI andmehalduse seminar. Zenodo. https://doi.org/10.5281/zenodo.8318151
• Pilvar, D. (2023, April 25). Licensing Research Outputs. Zenodo. https://doi.org/10.5281/zenodo.7863005
• Heleri Inno, & Diana Pilvar. (2022, November 8). How to make your messy data usable? - PART 2 Course. Zenodo. https://doi.org/10.5281/zenodo.7304308
• Heleri Inno. (2022, September 28). Licensing Research Outputs course. Zenodo. https://doi.org/10.5281/zenodo.7118427
• Heleri Inno. (2022, April 11). Metadata and README course. Zenodo. https://doi.org/10.5281/zenodo.6446879
• Heleri Inno. (2022, March 29).How to make your messy data usable? Course. Zenodo. https://doi.org/10.5281/zenodo.6393647
• Heleri Inno. (2021). The FAIR Principle Lecture Extra material (Version v1). Zenodo. https://doi.org/10.5281/zenodo.5769084
• Heleri Inno. (2021, October 15). The FAIR Principles Lecture - Autumn 2021 - in English. Zenodo. https://doi.org/10.5281/zenodo.5572352
• Inno, H. (2021, September 28). The FAIR Principles Lecture - Autumn 2021 - in Estonian. Zenodo. https://doi.org/10.5281/zenodo.5533534