BEGIN:VCALENDAR
VERSION:2.0
PRODID:icalendar-ruby
CALSCALE:GREGORIAN
BEGIN:VEVENT
DTSTAMP:20260527T085107Z
UID:d51073cb-68d4-4cc6-bcc3-69a4fb0c7ef5
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 man
 agement systems. \n\n* Create data analysis pipelines with Snakemake. \n\n
 * Combine Snakemake with containers to build reproducible computational pi
 pelines. \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 knowledge of UNIX co
 mmands and a good knowledge of software containers. In case of doubt\, eva
 luate your Unix skills with this [quiz](https://docs.google.com/forms/d/e/
 1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/viewform?usp=sf_l
 ink) before registering. \n\nYou should meet the learning outcomes of \n* 
 either [First Steps with UNIX in Life Sciences](https://www.sib.swiss/trai
 ning/course/20250902_FSWU) or the e-learning course [UNIX Fundamentals](ht
 tps://www.sib.swiss/training/course/2012_UNIXF)\n* and [Docker and Singula
 rity for Reproducible Research: Getting Started with Containers](https://w
 ww.sib.swiss/training/course/20260609_DOCKR) that takes place one day befo
 re this course.\n\n\n \n#### Technical \n\nParticipants are required to ha
 ve their own laptop with an installed modern code editor such as VScode.  
 \n\n \n\n# Schedule - CET time zone \n\n09:00 – 09:45: introduction to w
 orkflow management systems.  \n\n09:45 – 10:15: building a simple analys
 is pipeline with Snakemake. \n\n10:15 – 10:30: break. \n\n10:30 – 11:1
 5: 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 transfer
 ability.  \n\n13:30 – 14:00: complementing our workflow with a configfil
 e. \n\n14:00 – 14:30: combining Snakemake with conda and software contai
 ners. \n\n14:30 – 15:15: updating the analysis pipeline to use conda/con
 tainers. \n\n15:15 – 15:30: break. \n\n15:30 – 16:15: Snakemake in HPC
  environments. \n\n16:15 – 17:00: updating our workflow to send jobs via
  SLURM. \n\n\n\n# Application \n\nSIB courses usually open for application
 s 1-2 months before the course takes place. If not yet done\, we suggest y
 ou sign up for our mailing list here so that you are informed when the cou
 rses accept applications as some courses fill up very quickly.\n\nRegistra
 tion fees for academics are **100 CHF** and **500 CHF** for for-profit com
 panies. While participants are registered on a first come\, first served b
 asis\, exceptions may be made to ensure diversity and equity\, which may i
 ncrease the time before your registration is confirmed.\n\nApplications wi
 ll close on **02/06/2026** or as soon as the places will be filled up. Can
 cellation after **02/06/2026** will not be reimbursed.\n\nYou will be info
 rmed by email of your registration confirmation. Upon reception of the con
 firmation email\, participants will be asked to confirm attendance by payi
 ng 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 C
 EST.  \n\nMore information will be provided to the registered participants
  in due time.  \n\n \n \n\n#  Additional information \n\nCoordination: Gr
 égoire Rossier\, SIB Training group.\n\n \nAfter the course\, we will pro
 vide you with a Certificate of Attendance or a Certificate of Achievement 
 recommending 0.25 ECTS 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 workshops\, as well as all important deadlines using the form 
 [here](https://lists.sib.swiss/mailman/listinfo/courses). \n\n \nPlease no
 te that participation in SIB courses is subject to our [general conditions
 ](http://www.sib.swiss/training/terms-and-conditions). \n\n\nSIB abides by
  the [ELIXIR Code of Conduct](https://elixir-europe.org/events/code-of-con
 duct). Participants of SIB courses are also required to abide by the same 
 code. \n\n\n\nFor more information\, please contact [training@sib.swiss](m
 ailto://training@sib.swiss).
SUMMARY:Introduction to Snakemake for Reproducible and Scalable Research
URL;VALUE=URI:https://www.sib.swiss/training/course/20260610_%20INSNAK
END:VEVENT
END:VCALENDAR