Join researchers and enthusiasts for a wide-scope Bioinformatics Workshop Day that bridges biology, technology and society. From molecular insights to big data ethics, this event offers a unique opportunity to learn, discuss and connect across disciplines.
This multidisciplinary hands-on bioinformatics workshop invites PhD researchers and anyone interested in bioinformatics to spend a day exploring the rapidly evolving interface between life sciences and data science. The morning program features a series of lectures, perfect for those who want to learn without committing to the full-day event, while the afternoon offers optional, hands-on workshops for a deeper dive into specialized topics.
Bioinformatics and a changing society: Wide-scope bioinformatics workshop
4 December at 9.00-16.00
in Pub1 auditorium, Publicum
Program
08.30 Helpdesk for checking the installations of the programs needed for the workshops
09.00 Morning coffee
09.30 Welcome words
Heli Harvala, Faculty of Medicine
Saara Wittfooth, Faculty of Technology
09.35 Introduction to Bioinformatics
Anni Kauko, InFLAMES Flagship
10.00 Bioinformatics Applications in Medicine
Peter Simmonds, Faculty of Medicine
10.30 Big Data Applications and the Gut Microbiome
Matti Ruuskanen, Faculty of Technology
11.00 Legal Framework for Big Data and Bioinformatics
Tom Southerington, Faculty of Law
11.30 Lunch provided for workshop participants
12.30 Parallel workshops
14.30 Afternoon coffee
15.00 Wrap-up lectures
16.00 The day ends
After the lunch break (provided for participants staying on for the workshops) attendees can join one of five parallel sessions to explore specific themes in depth.
Please note that some workshops require prior bioinformatics knowledge, and all participants are expected to bring their own laptops with certain software installed beforehand. Take a look at the workshop descriptions from the dropdown menu from below.
- Public Health Microbiology – Peter Simmonds & Heli Harvala
- Spatial Transcriptomics – Lea Mikkola
- Basic R-Programming – Nick Booth & Anni Kauko
- Gut Microbiome – Tuomas Borman & Matti Ruuskanen
- Legal Aspects of Bioinformatics – Juha Vesala & Sini Mickelsson
The day will conclude with afternoon coffee and a joint wrap-up session, bringing together insights from the workshops and lectures alike.
While the morning lectures are open to everyone, the event requires registration due to limited capacity and catering. PhD researchers who participate in the full program and submit a learning diary afterward can earn 1 ECTS credit.
Register to the event at latest Wednesday 26 November:
Whether you’re new to bioinformatics or already working at its cutting edge, this event offers a rare opportunity to see the full scope of the field — from molecules to metadata, and from lab work to law.
Welcome everyone!
This course is arranged by the University of Turku Health, Diagnostics and Drug Development multidisciplinary theme.
Take a look at the workshop descriptions
This workshop will introduce you to the basic sequence analysis utilizing a practical case study based on a real-life example and will demonstrate the importance of bioinformatics in public health microbiology investigations. No prior experience is needed.
At the end of day, you will be able to construct multiple alignment and phylogenetic tree using different software (i.e. SSE and MEGA), understand the basics behind alignments and phylogenetic analysis, to be able to access different databases, and to be aware of the importance and potential future issues relating to bioinformatics and phylogeny within clinical virology and public health microbiology.
For this workshop, you need to have your own laptop with the following two software installed (MAC users will need to install Wine or other Windows emulator in order to install SSE):
- SSE Version 1.4 (freely downloadable from GitHub: https://github.com/psimmond/SSE)
- MEGA 12.0 (freely downloadable, select Windows, Graphical (GUI), version 12: http://megasoftware.net/)
Do not hesitate to contact if you have any questions or issues with installing the software!
More information from Heli Harvala (heli.harvala@utu.fi) and Peter Simmonds (peter.simmonds@utu.fi).
This workshop focuses on analysis of spatial transcriptomics data of human atherosclerotic aorta and carotid artery tissues. The participants will run a basic analysis pipeline in R (RStudio) and will learn the most important steps in the workflow, its limitations, and how to map candidate genes on tissue sections.
Prerequisites are: R basics (we will not use time to learn how to use the program), and a work/personal laptop either with ready access to CSC's Puhti super computer's interactive R environment and knowledge how to use it, or with R and Rstudio already installed. The data isn't massive, but the laptop needs to have moderate processing capacity (at least 8 Gb RAM, preferably more).
Helpful reading: Sun et al. paper (2023) https://doi.org/10.1016/j.jacc.2023.04.008, which utilizes similar data, and the preprint from Mikkola et al. (2025), which uses the same data the students will be working with: https://www.biorxiv.org/content/10.1101/2025.09.02.673686v1.full.pdf.
More information from Lea Mikkola (lea.mikkola@utu.fi)
This workshop is an introductory session to coding, covering the very basics of concepts that underpin practical computational science, using R as the example language. The session is ideal for those with no prior experience of coding, who perhaps have found the discipline too intimidating or confusing to approach and need a starting point. Researchers who have self-taught or used R programmes previously, but with no formal training, and would like to better understand how coding works will also find this session helpful.
Since this workshop will only be interacting with the basic functionalities of R, access to a simple installation of R and R Studio are the only requirements.
More information from Nick Booth (nicholas.booth@utu.fi).
Because of the complex nature of microbiome data, robust and reproducible computational approaches are essential. This workshop introduces the latest advances in microbiome analysis within Bioconductor, focusing on the mia (Microbiome Analysis) framework. Participants will gain hands-on experience with data handling, visualization, and analysis through a practical case study. The workshop will also introduce the Orchestrating Microbiome Analysis with Bioconductor online book (https://microbiome.github.io/OMA), a freely available resource that promotes best practices and supports adoption of the ecosystem. Together, these resources enable scalable, transparent, and community-driven microbiome data science.
Participants are expected to have some basic programming experience, for example, having written code in R or another programming language. No advanced programming or bioinformatics knowledge is required.
More information from Tuomas Borman (tuomas.v.borman@utu.fi)
This workshop addresses bioinformatics through the lense of certain legal issues. We will discuss topics such as data anonymization, conditions for using health data in AI development, and consent as a basis for using sensitive data from the perspective of how the legal framework can hinder or enable research and R&D. The workshop is intended to bring together experts from different fields, and no prior legal knowledge is expected. Participants can also propose topics for discussion when registering for the event.
More information from Juha Vesala (juha.vesala@utu.fi) and Sini Mickelsson (sini.mickelsson@utu.fi)
