Open Science at COS COS goes FOSS
Programme for 2025/26
(for the practical sessions registration is required - you can register to any of the courses here
2025-10-02 15:00-16:30 INF230 00.005
“COS goes FOSS - Introduction and Linux hacking session - Bring your computer!”
Gáspár Jékely, Sanja Jasek, David Hug, Benedikt Dürr
Do you have an old computer where you cannot update the OS? An oldish iMac maybe, where you cannot stream videos any more? A laptop running Windows 10 for which support will end soon? A Mac that is running super slow and you don’t understand why? If you bought a laptop or desktop after 2016, there is probably no need to buy a new one if your computer is running slow. The problem is probably with your OS and the update ratchet MS and Apple force on you. During this session, we will give an introduction into the powerful and free Linux OS and run a practical. You will be able to test Linux Mint from a flash drive, without installing it. Alternatively, you can directly jump into the FOSS ecosystem and install Linux on any laptop or desktop. Bring your old iMac, laptop, etc. Take the red pill! Experience OS freedom! Free your computer!
2025-10-17 whole day INF230 00.001
“Bonsai Workshop”
Mateusz Kostecki, Jagoda Nawrocka
A practical workshop to introduce the video acquisition and tracking tool
. Bonsai is a visual language for reactive programming. It is lightweight and easy to use with a variety of packages and modules for interfacing with hardware and for real-time processing and manipulation of data streams.2025-11-04 - 2025-11-05 whole day INF230 00.001
“RStudio paper/report/thesis-writing course”
Gáspár Jékely, Sanja Jasek
During this two-day course, we will give an introduction into how to use RStudio and Codeberg to write and collaborate on scientific reports or papers. The topics will include importing, tidying and plotting data (with ggplot2), assembling multi-panel figures with R code (cowplot, patchwork), writing reports and papers in Quarto (Rmarkdown), including referencing and embedding of figures. We will also learn version control of the project with git and collaboration and sharing via Codeberg and html annotation with hypothes.is and pCloud. This is not an introductory R course or an in-depth coding course, but a course on best practices and tools and approaches to work reproducibly on comprehensive reports or publication projects. The pipeline we will teach will also allow you to easily share your code, data and text as a research compendium when you publish a paper or a thesis. The course will teach how you can cross-reference everything in one project with relative paths, so that your project/paper is fully reproducible on other computers. Students, please register on HeiCo, others please
Tuesday, 10:00 - 18:00 on 04.11.2025 Kleiner Hörsaal (kHS) Wednesday, 09:00 - 13:00 on 05.11.2025 Kleiner Hörsaal (kHS) Wednesday, 14:30 - 18:00 on 05.11.2025 Kleiner Hörsaal (kHS)
2025-11-06 15:00-16:30 INF230 00.005
“Protein structure prediction with Boltz” Christine Schulz
During this session, Dr Christine Schulz, Research Software Engineer from the
will give an introduction into the history and methodology of 3D structural prediction algorithms (AlphaFold, Boltz) and a tutorial during which participants can use either online tools or try to install and run the FOSS structure prediction tool .2025-11-20 - 2025-11-21 whole day
“Tracking with DeepLabCut - Practical Course”
Konrad Danielewski
organised by COS goes FOSS & HD Open Lab
This two-day practical course will provide a deep dive into the powerful tracking tool DeepLabCut by one of its maintainers, Dr Konrad Danielewski. DeepLabCut can be used to track animal behaviour but also other timelapse data e.g. on plant root growth. You can bring your own data.
2025-11-27 15:00-16:30 INF230 00.005
“Protein structure visualisation and analysis with Pymol”
Christine Schulz
During this session, Dr Christine Schulz from the
will give an introduction into protein 3D structure visualisation tools (e.g. Pymol and some python packages). If you will attend the 3D structure prediction session, this one is also definitely recommended!2026-01-22 15:00-16:30 INF230 00.005
“Introduction to bioinformatic analysis with BioConductor”
Britta Velten
During this tutorial Britta Velten will introduce
, a collection of open source software packages for Bioinformatics. Bioconductor uses the R statistical programming language, and is open source and open development. There are 2341 software packages in Bioconductor release 3.21.2026-01-29 15:00-16:00 INF230 00.005
“The sorry state of scientific publishing and how we could move to an open and resilient infrastructure”
Gáspár Jékely
In this presentation Gáspár Jékely will give an overview of the scientific publishing landscape and why the current state damages scientific integrity and careers. He will also discuss how and why we need to move to a more open infrastructure controlled by scientists, libraries, universities and funding bodies.
2026-02-26 15:00-16:30 INF230 00.005
“Introduction into bash command line tools”
Sanja Jasek
This practical session will give an introduction into command line tools building up from the basics towards more advanced techniques. The topics will cover navigating on the CLI, ls, cd, pwd, find, grep, cut, tr, alias, pipes, loops, write to file (part 1), scripting - shebang, loops, tests, parameters, arrays, string substitution (part 2) traps, IO redirection, process substitution, stdin and stdout, how to give strings to programs that expect files and vice versa, gnu parallel (part 3). This first session will focus on part 1 and further sessions will be scheduled depending on the progress and the level of interest.
2026-03-26 14:00-16:30 and 2026-03-27 10:00-12:00 INF230 00.005
“Introduction to the handling of short read NGS data”
Christiane Kiefer
In this hands on course you will learn how to handle data from a simple Illumina sequencing experiment. You will be provided with sequencing data of which you briefly assess the quality and then trim your reads. You will map the reads to a reference, enhance mapping, call variants and generate a sequence containing the newly recovered SNPs. Finally you annotate your sequence by alignment. Although the course deals with a simple assembly of a plastid genome the methods you learn (or derivatives of them/similar methods/same principles) can be applied to a broad range of experiments dealing with Illumina data. Along with the practical work on the command line you will get to know a lot of the file formats you use when dealing with sequencing data and you will get an impression into how some of the algorithms you use actually work. You can work on your own linux machine but we can also provide access to a server for some participants where all software is installed.
2026-06-11 15:00-16:30 INF230 00.005
“Networks at COS and the university - use, abuse and basic cybersecurity”
Markus Kiefer
This workshop will focus on the security of our computational infrastructure. Topics will include an overview of the network landscape at the University (and) who has access to what etc.), useful network protocols and their pitfalls, firewalling, tunneling, VPNing. We will discuss what could go wrong and have an overview of the malware zoo and common vectors (like spear phishing and friends). In addition, you can learn about which role network connections play in that and a comparison between OSses in that respect. You will also get some advice about backup strategies (central backups and how to best complement with personal ones.)
further dates tbc.
Do you have an idea? Would you like to organise the next FOSS session? Please get in touch!
Related courses
Also check out the courses offered by Scientific Software Centre of the University.
All SSC Courses
If you are a BS/MS/PhD student, you can also register to our “Digital hygiene – how to use free open source software (FOSS) in your studies, research and teaching” course (7210WBW101 W).