BEGIN:VCALENDAR VERSION:2.0 PRODID:icalendar-ruby CALSCALE:GREGORIAN BEGIN:VEVENT DTSTAMP:20260830T204435Z UID:af7a9335-cf4d-40e6-b7ce-3ea60edaf023 DTSTART:20260610T090000Z DTEND:20260610T170000Z DESCRIPTION:# Overview \n\nReproducibility in research is essential to vali date scientific findings and build upon them. In the context of data analy sis\, this involves not only making code publicly available but also trans parently communicating the specific software libraries and tools used in t he analysis. To achieve this level of transparency and consistency\, this course introduces the Snakemake workflow management system combined with s oftware containers. Very briefly\, workflow management systems are designe d to create reproducible and scalable analysis pipelines\, streamlining th e process of managing complex computational tasks. Software containers are very powerful tools to ensure the same software is used across different computational platforms. By combining workflow management systems with sof tware containers\, the participants will learn a robust approach to mainta ining both reproducibility and scalability in their data analysis projects \, setting a strong foundation for reproducible scientific research. \n\nT he course material are in the dedicated [GitHub page](https://sib-swiss.gi thub.io/containers-snakemake-training/latest/).\n\n# Audience \n\nThis cou rse is designed for PhD students\, postdoctoral and other researchers in t he life sciences and bioinformaticians from both academia and industry who have an interest to increase the reproducibility of their work. \n\n# Lea rning outcomes \n\nAt the end of the course\, the participants are expecte d to: \n\n* **Understand** the basic principles and advantages of workflow management systems. \n\n* **Create** data analysis pipelines with Snakema ke. \n\n* **Combine** Snakemake with containers to build reproducible comp utational pipelines. \n\n* **Run** Snakemake pipelines locally and in HPC environments. \n \n\n# Prerequisites \n\n#### Knowledge / competencies \n\ nThis course is addressed to bioinformaticians with a basic to medium know ledge of UNIX commands and a good knowledge of software containers. In cas e of doubt\, evaluate your Unix skills with this [quiz](https://docs.googl e.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/v iewform?usp=sf_link) before registering. \n\nTo get the most out of this c ourse\, you should meet the learning outcomes of \n* either [First Steps w ith UNIX in Life Sciences](https://www.sib.swiss/training/course/20250902_ FSWU) or the e-learning course [UNIX Fundamentals](https://www.sib.swiss/t raining/course/2012_UNIXF)\n* and [Docker and Singularity for Reproducible Research: Getting Started with Containers](https://www.sib.swiss/training /course/20260609_DOCKR) that takes place one day before this course.\n\n\n \n#### Technical \n\nParticipants are required to have their own laptop w ith an installed modern code editor such as VScode. \n\n \n\n# Schedule - CET time zone \n\n09:00 – 09:45: introduction to workflow management sy stems. \n\n09:45 – 10:15: building a simple analysis pipeline with Snak emake. \n\n10:15 – 10:30: break. \n\n10:30 – 11:15: using wildcards to increase scalability. \n\n11:15 – 12:00: updating the analysis pipeline to increase scalability. \n\n12:00 – 13:00: lunch break. \n\n13:00 – 13:30: using configuration files to increase transferability. \n\n13:30 – 14:00: complementing our workflow with a configfile. \n\n14:00 – 14: 30: combining Snakemake with conda and software containers. \n\n14:30 – 15:15: updating the analysis pipeline to use conda/containers. \n\n15:15 – 15:30: break. \n\n15:30 – 16:15: Snakemake in HPC environments. \n\n 16:15 – 17:00: updating our workflow to send jobs via SLURM. \n\n\n\n# A pplication \n\nSIB courses usually open for applications 1-2 months before the course takes place. If not yet done\, we suggest you sign up for our mailing list here so that you are informed when the courses accept applica tions as some courses fill up very quickly.\n\nRegistration fees for acade mics are **100 CHF** and **500 CHF** for for-profit companies. While parti cipants are registered on a first come\, first served basis\, exceptions m ay be made to ensure diversity and equity\, which may increase the time be fore your registration is confirmed.\n\nApplications will close on **02/06 /2026** or as soon as the places will be filled up. Cancellation after **0 2/06/2026** will not be reimbursed.\n\nYou will be informed by email of yo ur registration confirmation. Upon reception of the confirmation email\, p articipants will be asked to confirm attendance by paying the fees within **5 days**.\n\n \n \n\n# Venue and Time \n\nThis course will be streamed.\ n\nThe course will start at 9:00 and end around 17:00 CEST. \n\nMore info rmation will be provided to the registered participants in due time. \n\n \n \n\n# Additional information \n\nCoordination: Grégoire Rossier\, SI B Training group.\n\n \nAfter the course\, we will provide you with a Cert ificate of Attendance or a Certificate of Achievement recommending 0.25 EC TS credits (given a passed exam).\n\n\nYou are welcome to register to the SIB courses mailing list to be informed of all future courses and workshop s\, as well as all important deadlines using the form [here](https://lists .sib.swiss/mailman/listinfo/courses). \n\n \nPlease note that participatio n in SIB courses is subject to our [general conditions](http://www.sib.swi ss/training/terms-and-conditions). \n\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-europe.org/events/code-of-conduct). Participants of SIB courses are also required to abide by the same code. \n\n\n\nFor mo re information\, please contact [training@sib.swiss](mailto://training@sib .swiss). SUMMARY:Introduction to Snakemake for Reproducible and Scalable Research URL;VALUE=URI:https://www.sib.swiss/training/course/20260610_INSNAK END:VEVENT END:VCALENDAR