Course Description
Teaching Methods:
- Theoretical sessions: Introduce key concepts with examples of real-world applications in bioinformatics (the theory part will be interspersed along all workshop)
- Practical sessions: Hands-on exercises with Conda, Docker, and Jupyter Notebooks.
- Case studies: Practical examples of how these tools are used in collaborative research projects.
- Interactive Q&A and problem-solving workshops: Address specific challenges participants may encounter in their own workflows.
Important Dates
- Deadline for applications: 4 november 2024
- Chosen participants will be notified by: 16 november 2024
- Course date: 26th November 2024
Venue
The course is especially dedicated to selected participants to the BBCC 2024 conference https://www.bbcc-meetings.it/bbcc2024/
The course will be held at CNR – Consiglio Nazionale delle Ricerche Via Pietro Castellino 111 – 80131 Napoli (NA), Italy Link to the maps
Fee
The course does not include a fee
Selection
The course is especially dedicated to selected participants to the BBCC 2024 conference https://www.bbcc-meetings.it/bbcc2024/
A maximum of 15 candidates will be selected on the basis of an assessment of their knowledge and skills. Selected participants will be notified by 16 november 2024
Instructor
- Dott. Raoul Bonnal, IFOM – Research Computing & Data Science Manager
Helpers
- Dott. Riccardo Lorenzo Rossi, Bioinformatics scientist, IFOM-ETS, Research Computing & Data Science
- Dott. Cristiano Petrini, Bioinformatics engineer, IFOM-ETS, Research Computing & Data Science
Organisers
- Prof. Anna Marabotti, University of Salerno, ELIXIR-IT, Italy
- Prof. Allegra Via, University of Rome “La Sapienza”, ELIXIR-IT, Italy
- Dott. Angelo Facchiano, CNR-ISA, Avellino, Italy
Contact
For all kinds of queries, please contact the organizer Anna Marabotti or Angelo Facchiano, or please write to Elixir_training_email.
Aims of the workshop
- To provide participants with a foundational understanding of software environments, containerisation, and notebooks for managing computational workflows;
- To introduce tools that support reproducibility, portability, and efficiency in bioinformatics research;
- To offer practical skills in deploying and managing environments, using containers, and working with Jupyter notebooks.
Resources and tools covered
- Conda environments and their installation
- Conda channels (bioconda, conda-forge)
- Containers (Docker)
- Integration of containers and conda environments
- Markdown scripting, JupyterHub and Jupyter notebooks
Learning Outcomes
After completing this course, participants will be able to:
- Set up and manage isolated software environments using Conda;
- Build, deploy, and use containers;
- Create and share reproducible analyses using Jupyter Notebooks;
- Understand the importance of these tools for collaborative and reproducible research.
Course prerequisites
Basic Knowledge of Unix. Linux/Windows/OSX are fine. An assessment questionnaire will be sent for the selection of participants