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DTSTAMP:20260906T054959Z
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DTSTART:20251010T090000Z
DTEND:20251010T170000Z
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\nYou should meet
  the learning outcomes of either [First Steps with UNIX in Life Sciences](
 https://www.sib.swiss/training/course/20250902_FSWU) or the e-learning cou
 rse [UNIX Fundamentals](https://www.sib.swiss/training/course/2012_UNIXF) 
 and [Docker and Singularity for Reproducible Research: Getting Started wit
 h Containers](https://www.sib.swiss/training/course/20251009_DOCK).\n\nThi
 s course is addressed to bioinformaticians with a basic to medium knowledg
 e of UNIX commands and a good knowledge of software containers. In case of
  doubt\, evaluate your Unix skills with this [quiz](https://docs.google.co
 m/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoBKNB27MQ/viewf
 orm?usp=sf_link) before registering. \n \n\n#### Technical \n\nParticipant
 s are required to bring their own laptop with an installed modern code edi
 tor 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: bui
 lding a simple analysis pipeline with Snakemake. \n\n10:15 – 10:30: brea
 k. \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 work
 flow with a configfile. \n\n14:00 – 14:30: combining Snakemake with cond
 a and software containers. \n\n14:30 – 15:15: updating the analysis pipe
 line 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 work
 flow to send jobs via SLURM. \n\n\n\n# Application \n\nSIB courses usually
  open for applications 1-2 months before the course takes place. If not ye
 t done\, we suggest you sign up for our mailing list here so that you are 
 informed when the courses accept applications as some courses fill up very
  quickly.\n\nRegistration fees for academics are **100 CHF** and **500 CHF
 ** for for-profit companies. While participants are registered on a first 
 come\, first served basis\, exceptions may be made to ensure diversity and
  equity\, which may increase the time before your registration is confirme
 d.\n\nApplications will close as soon as the places will be filled up\, un
 til **01/10/2025**. Deadline for free-of-charge cancellation is set to **2
 6/09/2025**. Cancellation after this date will not be reimbursed.\n\nYou w
 ill be informed by email of your registration confirmation. Upon reception
  of the confirmation email\, participants will be asked to confirm attenda
 nce by paying the fees within 5 days.\n\n \n \n\n# Venue and Time \n\nThis
  course will be held online\n\nThe course will start at 9:00 and end aroun
 d 17:00 CEST.  \n\nMore information will be provided to the registered par
 ticipants in due time.  \n\n \n \n\n#  Additional information \n\nCoordina
 tion: Diana Marek\, SIB Training group.\n\nHelper: Joana Carlevaro\n \nWe 
 will recommend 0.25 ECTS credits for this course (given a passed exam at t
 he end of the course). \n\n\nYou are welcome to register to the SIB course
 s mailing list to be informed of all future courses and workshops\, as wel
 l as all important deadlines using the form [here](https://lists.sib.swiss
 /mailman/listinfo/courses). \n\n \nPlease note that participation in SIB c
 ourses is subject to our [general conditions](http://www.sib.swiss/trainin
 g/terms-and-conditions). \n\n\nSIB abides by the [ELIXIR Code of Conduct](
 https://elixir-europe.org/events/code-of-conduct). Participants of SIB cou
 rses are also required to abide by the same code. \n\n\n\nFor more informa
 tion\, 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/20251010_SNAKE
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