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Summer school in bioinformatics 2023 is a unique event that empowers students to grow and develop as they discover new skills and interests. It strives to create an inspiring environment that will lead to outstanding learning experience and endless memories.

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This year the summer school will be held from 17-21st July at the Biotechnical faculty of the University of Ljubljana in Ljubljana, Slovenia


July 2023 - we have accepted the applicants!

please find your homework!

Course content

Day 1:

Introduction to the command line, the conda package manager and the bash scripting language. Downloading and annotating.


9:00 – 9:15   Introduction and course overview

9:15 – 10:00: Interactive lecture [Le1]: setting up the command line (prior Linux install is expected)

10:00 – 12:00: Interactivate Linux exercises – navigating, copying and loops

12:00 – 13:00: Lunch

13:00 – 14:00: Lecture [Le2]: Basic genome assembly and what we can download.

14:00 – 15:00: Genome download & overview – how & what software?

15:00 – 17:00: Genome annotation – new environments and our first loop


Day 2:

Finding the functional gene content and building a phylogeny

9:00 – 9:30:   Recap and follow up [Le3] – the hard parts of bioinformatics?

9:30 – 10:00: Lecture [Le4] – annotation of phages and BGCs

10:00 – 11:00: Prophage annotation – another loop, another package

11:00 – 12:00: BGC annotation – yet another loop and a different package

12:00 – 13:00: Lunch

13:00 – 14:00: Phylogeny, Trees and Genotypes [Le5]

14:00 – 16:00: Building a core genome phylogenetic tree and finding patterns


Day 3: A trip to Bela krajina

A trip to the Kolpa river and student presentations.


Day 4: Amplicon sequencing

Introduction to R and Rstudio, installing R packages. The concepts of metataxonomics and the DADA2 pipeline


9:00 – 9:15      Recap and follow up

9:15 – 10:00:   Interactive lecture [Le6]: setting up Rstudio projects

10:00 – 11:00: Interactivate R exercises – navigating, installing and plotting

11:00 – 12:00: Lecture [Le7]: Metataxonomics as a concept.

12:00 – 13:00: Lunch

13:00 – 16:00: Downloading and bioinformatic analysis of data

16:30 Genialis company presentation


Day 5: Amplicon sequencing

Statistical analysis of metataxonomic data.

9:00 – 9:30:     Recap and follow up

9:30 – 12:00:    Statistical analysis of metataxonomic data [Le8]

12:00 – 13:00: Lunch

13:00 – 16:00: Univariate and multivariate analysis [Le9]   



Whole genome comparisons
Genome annotation
Secondary metabolites

Phage extraction
Phage clustering
Amplicon sequencing from start to finish


Summer School fee

The fee for this year's school is 100 eur. What do you get for this?

Online Class


First of all, you get 5 days of lectures  and an opportunity to learn new skills from a highly experienced teacher, that you can use at your (future) work, as a part of your graduation thesis or just for fun. 

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You will gain experience in meeting new peers, at presenting your data as well as new possible future collaborators, maybe even your future thesis mentor.

Summer Fun


Throughout the school we will try to mingle and interact as much as we can,  and we will have a boat trip through the center of Ljubljana.



We will provide snacks, refreshments, fruits, chocolate and one warm meal.


Večna pot 111, 1000 Ljubljana, Slovenia

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Our biggest supporter is Biotechnical faculty of University of Ljubljana. Apart from the faculty we have support from:



Genialis is a data science company putting people first to develop more effective drugs, and to allow us to make more targeted treatment decisions for better outcomes.
People First embodies our commitment to personalizing medicine for the benefit of patients by modeling fundamental biology through the use of human data. It is also Genialis’ principal core value, the north star of how we build our team and orchestrate our work lives.



Slovenian microbiological society. The Slovenian Microbiological Society (SMD) is a prestigious scientific organization dedicated to advancing microbiology in Slovenia. It serves as a platform for collaboration among microbiologists from various fields. The SMD organizes conferences and workshops, facilitating the exchange of ideas and promoting interdisciplinary collaborations. It supports the professional development of its members through grants, scholarships, and awards.



JAFRAL is an independent Contract Manufacturing Organization (CMO) & Contract Research Organization (CRO). JAFRAL is world’s only CMO that its primary focus is production of non-GMP and GMP bacteriophages. JAFRAL is an ideal outsourcing partner, since they ensure that their customers have time to focus on its own areas of expertise where JAFRAL is taking care of CMC (Chemistry, Manufacturing and Control) activities.

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