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DTSTART:20250528T090000Z
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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\nYou should meet the learning outcomes of either [First Steps with
  UNIX in Life Sciences](https://www.sib.swiss/training/course/20240912_FSW
 U) or the e-learning course [UNIX Fundamentals](https://www.sib.swiss/trai
 ning/course/2012_UNIXF) and [Docker and Singularity for Reproducible Resea
 rch: Getting Started with Containers](https://www.sib.swiss/training/cours
 e/20250527_DOCK).\n\nThis course is addressed to bioinformaticians with a 
 basic to medium knowledge of UNIX commands and a good knowledge of softwar
 e containers. In case of doubt\, evaluate your Unix skills with this [quiz
 ](https://docs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYB
 bhBiaqcaHoBKNB27MQ/viewform?usp=sf_link) before registering.\n \n\n#### Te
 chnical \n\nParticipants are required to bring their own laptop with an in
 stalled 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: building 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 incre
 ase scalability. \n\n12:00 – 13:00: lunch break. \n\n13:00 – 13:30: us
 ing configuration files to increase transferability.  \n\n13:30 – 14:00:
  complementing our workflow with a configfile. \n\n14:00 – 14:30: combin
 ing Snakemake with conda and software containers. \n\n14:30 – 15:15: upd
 ating the analysis pipeline to use conda/containers. \n\n15:15 – 15:30: 
 break. \n\n15:30 – 16:15: Snakemake in HPC environments. \n\n16:15 – 1
 7:00: updating our workflow to send jobs via SLURM. \n\n \n \n\n# Applicat
 ion \n\nThe registration fees for academics are **100 CHF** and **500 CHF*
 * for for-profit companies. \n\n \n \n\nWhile participants are registered 
 on a first come\, first served basis\, exceptions may be made to ensure di
 versity and equity\, which may increase the time before your registration 
 is confirmed. \n\n \n \n\nYou will be informed by email of your registrati
 on confirmation. Upon reception of the confirmation email\, participants w
 ill 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 wi
 ll be filled up. Deadline for free-of-charge cancellation is set to *14/05
 /2025*. Cancellation after this date will not be reimbursed. Please note t
 hat participation in SIB courses is subject to our [general conditions](ht
 tp://www.sib.swiss/training/terms-and-conditions). \n\n \n \n\n# Venue and
  Time \n\nThe course will be held in Zurich (UZH\, Campus Irchel). \n\n \n
 \nThe course will start at 9:00 and end around 17:00.  \n\n \n \n\nMore in
 formation will be provided to the registered participants in due time.  \n
 \n \n \n\n#  Additional information \n\nCoordination: Valeria Di Cola\, SI
 B 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 mailing list to be informed of all
  future courses and workshops\, as well as all important deadlines using t
 he form [here](https://lists.sib.swiss/mailman/listinfo/courses). \n\n \n 
 \n\nPlease note that participation in SIB courses is subject to our [gener
 al conditions](http://www.sib.swiss/training/terms-and-conditions). \n\n \
 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 \n\nFor more information\, please contact
  [training@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Reproducible and Scalable Research with Snakemake and Software Cont
 ainers
URL;VALUE=URI:https://www.sib.swiss/training/course/20250528_SNAKE
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