Building Agentic AI Applications for Biodata Exploration

Overview

This one-day course introduces life scientists and bioinformaticians to agentic AI and how to apply it to the exploration of biological data. It begins with the foundations of large language models and coding agents, covering how agents work, how they can be extended with tools through open standards such as the Model Context Protocol (MCP). A large part of the day is hands-on: participants connect AI agents to established bioinformatics resources to answer biological questions, build a simple agentic application of their own in Python, and create their own MCP server that makes a biological database accessible to AI agents.

This course is organized in the context of the ELIXIR-IMPACT project, a collaboration between the Czech and Swiss ELIXIR nodes. The course is organized by experts from both countries and takes place in both Prague and Lausanne, with a virtual connection between the rooms. Attendance is free, but participants need to apply, and only selected participants can join.

Audience

This course is designed for PhD students, postdoctoral and other researchers in the life sciences from both academia and industry who are interested in LLMs and who already have prior experience using Python.

Learning outcomes

At the end of the course, the participants are expected to:

• Understand the basics of Large Language Models
• Explore the interplay of LLMs and bioinformatics knowledge bases
• Develop tools and skills to enable AI agents to interact with bioinformatics knowledge bases
• Programmatically interact with LLMs in a Python Notebook
• Build a simple agentic application for answering questions over biodata

Prerequisites

Knowledge / competencies

Participants should have at least one year of additional experience using Python.

Technical

You will need access to a computer with WI-FI enabled.

Participants can work on a cloud environment with all required software preinstalled. Further details will be communicated before the course.

Application

Attendance is free, but participants need to apply, and only selected participants can join. Apply for the course using a form (will be added when registration opens) before November 30th. The selection decision will be communicated before December 4th.

Venue and Time

This course will take place at the University of Lausanne, and at the University of Chemistry and Technology in Prague. Participants can choose where to attend.

The course will start at 9:00 CET and end around 17:00 CET.

Precise information will be provided to the registered participants in due time.

Additional information

Coordination: Geert van Geest, SIB training group.

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.