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SUMMARY:Building Agentic AI Applications for Biodata Exploration
UID:https://www.elixir-czech.cz/events/building-agentic-ai-applications-for-biodata-exploration-2026
LOCATION:
DTSTAMP:20270118T090000
DTSTART;TZID=Europe/Prague:20270118T090000
DTEND;TZID=Europe/Prague:20270119T170000
DESCRIPTION:OverviewThis 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. AudienceThis 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.SpeakersVincent Emonet (SIB)Panayiotis Smeros
(SIB)Michaela Liegertová (IMG/UJEP)Lukáš Hejtmánek (MU)Vojtěch Bystrý
(MU)Learning outcomesAt the end of the course, the participants are
expected to:Understand the basics of Large Language ModelsExplore the
interplay of LLMs, agents and bioinformatics knowledge basesDevelop agentic
applications to interact with these knowledge basesApply good practices for
setting up, restricting and monitoring coding agents, including keeping
context and token use under controlUnderstand how agents can run on
open-weight models in a trusted research environment when working with
sensitive dataUse an agent to put together existing bioinformatics tools
and workflows and deploy them on a compute clusterUse a coding agent to
create interactive visualizations and dashboards from analysis
resultsPrerequisitesKnowledge / CompetenciesBasic understanding of Python,
running commands in the terminal and working on a remote machine through an
interface.TechnicalYou 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.ApplicationAttendance 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
TimeThis 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 informationCoordination: 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.		
																
															
																
															
		Co-organized by
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