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DTSTAMP:20260808T161632Z
UID:820a2c7e-4f90-4204-9821-e2b0ac1cb726
DTSTART:20250528T090000Z
DTEND:20250528T170000Z
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\n#
  Audience \n\nThis course is addressed to all bioinformaticians developing
  computational pipelines with an interest to increase the reproducibility 
 of their work. \n\n# Learning outcomes \n\nAt the end of the course\, the 
 participants are expected to: \n\n* Understand the basic principles and ad
 vantages of workflow management systems. \n\n* Create data analysis pipeli
 nes with Snakemake. \n\n* Combine Snakemake with containers to build repro
 ducible computational pipelines. \n\n* Run Snakemake pipelines locally and
  in HPC environments. \n \n\n# Prerequisites \n\n#### Knowledge / competen
 cies \n\nThis course is addressed to bioinformaticians with a basic to med
 ium knowledge of UNIX commands. In addition\, participants are expected to
  either have participated in one of our container courses or have a good k
 nowledge of software containers.  \n \n\n#### Technical \n\nParticipants a
 re required to bring 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 workflow management systems.  \n\n09:45 – 10:15: buildi
 ng a simple analysis pipeline with Snakemake. \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 workf
 low with a configfile. \n\n14:00 – 14:30: combining Snakemake with conda
  and software containers. \n\n14:30 – 15:15: updating the analysis pipel
 ine to use conda/containers. \n\n15:15 – 15:30: break. \n\n15:30 – 16:
 15: Snakemake in HPC environments. \n\n16:15 – 17:00: updating our workf
 low to send jobs via SLURM. \n\n \n \n\n# Application \n\nThe registration
  fees for academics are **100 CHF** and **500 CHF** for for-profit compani
 es. \n\n \n \n\nWhile participants are registered on a first come\, first 
 served basis\, exceptions may be made to ensure diversity and equity\, whi
 ch may increase the time before your registration is confirmed. \n\n \n \n
 \nYou will be informed by email of your registration confirmation. Upon re
 ception of the confirmation email\, participants will be asked to confirm 
 attendance by paying the fees within 5 days. \n\n \n \n\nApplications will
  close on *14/05/2025* or as soon as the places will be filled up. Deadlin
 e for free-of-charge cancellation is set to *14/05/2025*. Cancellation aft
 er this date will not be reimbursed. Please note that participation in SIB
  courses is subject to our [general conditions](http://www.sib.swiss/train
 ing/terms-and-conditions). \n\n \n \n\n# Venue and Time \n\nThe course wil
 l be held in Zurich. \n\n \n\nThe course will start at 9:00 and end around
  17:00.  \n\n \n \n\nMore information will be provided to the registered p
 articipants in due time.  \n\n \n \n\n#  Additional information \n\nCoordi
 nation: Valeria Di Cola\, SIB Training Group.\n\n \n \n\nWe will recommend
  0.25 ECTS credits for this course (given a passed exam at the end of the 
 course). \n\n \n \n\nYou are welcome to register to the SIB courses mailin
 g 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 \n \n\nPlease note that participation in SIB cour
 ses is subject to our [general conditions](http://www.sib.swiss/training/t
 erms-and-conditions). \n\n \n \n\nSIB abides by the [ELIXIR Code of Conduc
 t](https://elixir-europe.org/events/code-of-conduct). Participants of SIB 
 courses are also required to abide by the same code. \n\n \n \n\nFor more 
 information\, please contact [training@sib.swiss](mailto://training@sib.sw
 iss).
SUMMARY:Reproducible and Scalable Research with Snakemake and Software Cont
 ainers
URL;VALUE=URI:https://www.sib.swiss/training/course/20250601_SNAKE
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