Overview

This two-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 and how to extend them with tools via open standards such as the Model Context Protocol (MCP). A large part of the first 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. On the second day, participants move from building agents to using them responsibly in real analyses. It starts with good practices for working with coding agents, both commercial and open: how to set them up, how to restrict what they can do, how to monitor and check their actions, and how to keep context and token use under control. Participants then see how agents can run on open-weight models inside a trusted research environment, so they can be used safely with sensitive data. The hands-on part covers two use cases: an agent that puts together existing tools and workflows and deploys them on a compute cluster (Kubernetes), and a coding agent that turns tabular analysis results into interactive plots and dashboards.

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-person in Prague and Lausanne, with a virtual connection between the two locations. 

Audience

This course is designed for PhD students, postdoctoral researchers, and other researchers in the life sciences from both academia and industry who work with biodata resources and are interested in using agentic AI to explore them.

Speakers

• Vincent Emonet (SIB)
• Panayiotis Smeros (SIB)
• Michaela Liegertová (IMG/UJEP)
• Lukáš Hejtmánek (MU)
• Vojtěch Bystrý (MU)

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, agents and bioinformatics knowledge bases
• Develop agentic applications to interact with these knowledge bases
• Apply good practices for setting up, restricting and monitoring coding agents, including keeping context and token use under control
• Understand how agents can run on open-weight models in a trusted research environment when working with sensitive data
• Use an agent to put together existing bioinformatics tools and workflows and deploy them on a compute cluster
• Use a coding agent to create interactive visualizations and dashboards from analysis results

Prerequisites

Knowledge / Competencies

Basic understanding of Python, running commands in the terminal and working on a remote machine through an interface.

Technical

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

Participants will be given access to a cloud environment with all required software preinstalled. Further details will be communicated before the course.

Application

Attendance is free, but participants must apply, and only selected applicants can join. Selection will be based on their motivation and on how well they align with the intended learning outcomes and target audience. Apply for the course using this form before November 29th. The selection decision will be communicated on December 4th. ELIXIR-IMPACT cannot provide financial support for travel.

Venue and Time

This course will take place in-person 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 for 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.