Summer school in Bioinformatics 2024​

Join us in this adventure! This year the summer school will be

held from 8-12th July at the Biotechnical faculty of the

University of Ljubljana in Ljubljana, Slovenia


Applications close on 10th June


The overall teaching aims of the summer school is to create competence in the students in terms of independently performing bioinformatic analysis on the command line. This includes comparative analysis on bacterial (meta)-genomes and metataxonomic analysis. A student will learn through examples from practice, how to analyse genetic content within bacterial organisms and engage in discussions regarding the biological implications stemming from phylogenetic relationships, genetic content, microbial composition, and their interrelationships. The programme of summer school represents the combination of knowledge from the fields of informatics and biology and focuses on individual practical work in an international group of students. The target participants are students of Microbiology, Biotechnology, Biology, Genetics (BSc, MSc, PhD students).


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Students will gain proficiency in utilizing the Linux command line, demonstrate competence in utilizing recommended command line tools and be able to conduct literature reviews in bioinformatics to identify additional tools pertinent to addressing biological inquiries. They will also be able to determine the composition of microbiomes through analytical techniques and analyse genetic content within bacterial organisms to deduce biological significance. They will engage in discussions regarding the biological implications stemming from phylogenetic relationships, genetic content, microbial composition, and their interrelationships.

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Over the course of the summer school, participants will delve into the intricate world of genomic assembly, annotation, and metagenomic analysis. In general, the assembly of genomes using short reads (SPAdes), long reads (Flye), and hybrid approaches (Unicycler), followed by genome annotation using Bakta will be addressed. Functional profiling of genomes will be covered, focusing on secondary metabolites prediction (antiSMASH) and carbohydrate-active enzymes (CAZYmes) annotation with dbCAN. Next, participants will venture into long-read metagenomics, learning to assemble small metagenomes with metaFlye and taxonomically classify metagenomic contents using 16S rRNA amplicon sequencing (barrnap) and kmer-based methods (Kraken2). The week will conclude with insights into taxonomic analysis of microbiomes, including 16S rRNA amplicon sequencing data classification (DADA2), visualization, and statistical analysis of microbiome data using vegan. 

About us

I am Polonca Stefanic, an assistant professor at the Biotechnical faculty, University of Ljubljana. In the summer of 2021 I organized the first summer school in bioinformatics, which took place at the Biotechnical Faculty of the University of Ljubljana, in July (19-23.7.2021). 

I have extensive experience in B. subtilis quorum sensing, but now my biggest passion resides in kin discrimination and its consequences on the survival, horizontal transfer and evolution of this species. I am also involved in a project investigating Bacillus strains as potential plant growth promoters (PGP), where we isolate and test new strains for PGP and biocontrol activity against different bacterial pathogens. Besides, I take part in an inter-species interaction project, where we test the ability of Bacillus species to act against Campylobacter in different setting. Always open to new collaborations and enjoy visiting research labs as a foreign scholar. Recently I started introducing bioinformatics to my work and through collaborations I have met many excellent teachers and experts in the field, allowing me to invite them to the school as lecturers.

Together with dr. Mikael Lenz Strube we are hosting the Summer school in bioinformatics. His research is focused on the prevention of post weaning diarrea in pigs, mainly through prebiotics and other non-medical methods. He is furthermore interested in carbohydrate chemisty, enzymology, the microbiota of the intestines and advanced statistical analysis. He has numerous publications related to NGS, metagenomics and comparative genomic.

Prof. dr. Mikael Lenz Strube
Ass. prof. dr. Polonca Stefanic

Where are we?

Summer school in bioinformatics 2024 will be held in a beautiful city of Ljubljana, Slovenia, at the Biotechnical faculty of the University of Ljubljana.



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