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DTSTART:20231012T090000Z
DTEND:20231013T170000Z
DESCRIPTION:# Overview\n\nReproducible data analysis in bioinformatics goes
  beyond good documentation and sharing code. Often\, analyses depend on di
 fferent compute environments and workflows with many programs\, libraries\
 , and settings. Containers and workflow management systems can help you or
 ganizing your environments and workflows\, and therefore make your work mo
 re reproducible and efficient. Container software like Docker and singular
 ity enable you to store\, reuse\, and share your environments\, while work
 flow management systems like Snakemake enable you to integrate environment
 s and scripts in a single scalable and reproducible workflow.  \n\nTo intr
 oduce you to working with containers and workflow management systems in th
 e context of bioinformatics research\, we will take a practical approach w
 ith several hands-on exercises to go through the basics of using\, develop
 ing\, and sharing containers and workflows. \n\n# Audience\nThis course is
  addressed to bioinformaticians and life scientists that are doing bioinfo
 rmatic analyses and want to get introduced to containers and pipelines. \n
 \n# Learning outcomes\nAt the end of the course\, the participants are exp
 ected to:\n* Understand the basic concepts and terminology associated with
  virtualization with containers \n* Customize\, store\, manage and share c
 ontainerized environments with Docker \n* Use Singularity to run container
 s on a shared computer environment (e.g. a HPC cluster) \n* Understand the
  basic concepts and terminology associated with workflow management system
 s \n* Create a computational workflow that uses containers with Snakemake 
 \n\n# Prerequisites\n##### Knowledge / competencies\nThis course is design
 ed for those interested to work with containers and pipelines in the conte
 xt of bioinformatics. Practical experience on the basic UNIX commands is r
 equired. You can test your skills with Unix with the quiz [here](https://d
 ocs.google.com/forms/d/e/1FAIpQLSd2BEWeOKLbIRGBT_aDEGPce1FOaVYBbhBiaqcaHoB
 KNB27MQ/viewform?usp=sf_link). If you do not feel comfortable with UNIX co
 mmands\, you can refresh your knowledge with our [UNIX fundamentals](https
 ://edu.sib.swiss/pluginfile.php/2878/mod_resource/content/4/couselab-html/
 content.html) e-learning module. \n\n##### Technical\nYou are required to 
 bring your own laptop with [Docker pre-installed](https://docs.docker.com/
 get-docker/) and have created an account on [dockerhub](https://hub.docker
 .com/). Note that you need admin rights in your computer to install and us
 e Docker. Windows users will find a recent version of Docker Desktop [here
 ](https://docs.docker.com/docker-for-windows/install/). \n\nYou should als
 o have a modern code editor installed\, like [Sublime Text](https://www.su
 blimetext.com/) or [VScode](https://code.visualstudio.com/).\n\n\n\n# Appl
 ication\n\n\n\n\nRegistration fees for academics are **200 CHF** and **100
 0 CHF** for for-profit companies. While participants are registered on a f
 irst come\, first served basis\, exceptions may be made to ensure diversit
 y and equity\, which may increase the time before your registration is con
 firmed. \n\nApplications will close as soon as the places will be filled u
 p. Deadline for free-of-charge cancellation is set to **September 22\, 202
 3**. Cancellation after this date will not be reimbursed. Please note that
  participation in SIB courses is subject to our [general conditions](https
 ://www.sib.swiss/training/terms-and-conditions). \n\nYou will be informed 
 by email of your registration confirmation. Upon reception of the confirma
 tion email\, participants will be asked to confirm attendance by paying th
 e fees within 5 days. \n\n# Venue and Time\nThis course will be held at th
 e Swiss Institute of Allergy and Asthma Research (SIAF) in Davos. \n\nThe 
 course will start at 9:00 CET and end around 17:00 CET.  \n\nPrecise infor
 mation will be provided to the participants in due time.\n\n#  Additional 
 information\nCoordination: Monique Zahn\, SIB Training Group.\n\nWe will r
 ecommend 0.5 ECTS credits for this course (given a passed exam at the end 
 of the course).\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 i
 mportant deadlines using the form [here](https://lists.sib.swiss/mailman/l
 istinfo/courses).\n\nPlease note that participation in SIB courses is subj
 ect to our [general conditions](https://www.sib.swiss/training/terms-and-c
 onditions).\n\nSIB abides by the [ELIXIR Code of Conduct](https://elixir-e
 urope.org/events/code-of-conduct). Participants of SIB courses are also re
 quired to abide by the same code.\n\nFor more information\, please contact
  [training@sib.swiss](mailto://training@sib.swiss).
SUMMARY:Introduction to Containers and Snakemake for Reproducible Research
URL;VALUE=URI:https://www.sib.swiss/training/course/20231012_ICWRR
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