Training courses 2024: Software Environments, Containers, and Notebooks (for Bioinformatics and Computational Biology)

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.

Target audience

The target audience is (computational) biologists or bioinformaticians who are familiar with basic computational analysis but want to improve their skills in managing software environments, using containers, and working with notebooks. The course is ideal for those looking to streamline their workflows, ensure reproducibility, and effectively collaborate on computational projects.

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

Registration

Application Form

Programme