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DTSTAMP:20260618T110847Z
UID:508d1539-823f-4287-b0d0-38f23081c98b
DTSTART:20251105T090000Z
DTEND:20251126T170000Z
DESCRIPTION:IMPORTANT: this course will take place on 4 afternoons\, at 5\,
  12\, 19 and 26 November 2025\n\n\n# Overview\nScripting allows shell user
 s to automate repetitive tasks\, thus improving reproducibility\, reducing
  the risk of errors\, freeing time\, and avoiding boredom.\n\nBioinformati
 cs analysis pipelines may involve dozens or hundreds of steps that are eac
 h carried out by different command-line programs: assembling these into sc
 ripts allows users to treat whole pipelines as if they were ordinary shell
  commands.\n\n# Audience\nThis course targets UNIX users who have basic kn
 owledge of interactive shell use (such as taught in the SIB's [First Steps
  with UNIX in Life Sciences](https://www.sib.swiss/training/course/2024011
 6_FSWU)) and are interested in moving from interactive to automated tasks.
 \n\n# Learning objectives\nAt the end of the course\, the participants sho
 uld be able to:\n\n* Explain how Bash processes input\, distinguishing in 
 particular between the different types of expansion and their purposes\n* 
 Differentiate between the various syntactic constructs of Bash\, identifyi
 ng their purposes and how they are used\n* Integrate knowledge of tests\, 
 conditionals\, loops\, functions\, as well as the various forms of expansi
 on  and other features of Bash to create a script that solves a given prob
 lem. \n\n\n\n# Prerequisites\n**Knowledge / competencies**\n\nThis course 
 is designed for intermediate level users. They are expected to know how to
  use a Unix shell interactively\, i.e.\, moving around the filesystem\, un
 derstanding pathnames\, launching programs that work on data\, redirecting
  output to files or other programs\, etc.\nThey are also expected to have 
 some familiarity with basic shell utilities like grep\, cut\, tr\, etc (al
 though no expert skills are required).\nNotions of programming (in any lan
 guage) will be useful\, but not essential.\nFinally\, some proficiency wit
 h a text editor is a must.\n\nMore details [here](https://sibcloud-my.shar
 epoint.com/:b:/r/personal/patricia_palagi_sib_swiss/Documents/TrainingGrou
 p-Shared/Courses/2024/20240522_ADVUN/prerequisites.pdf?csf=1&amp\;web=1&am
 p\;e=BFfujJ)\n\n\n\n\n**Technical**\n\nA laptop with a command line termin
 al and a recent version of Bash (4.0 or newer should be ok) installed. The
  alternative for Windows users is to activate [WSL/WSL2](https://learn.mic
 rosoft.com/en-us/windows/wsl/about).\n\n# Application\n\nRegistration fees
  for academics are **200 CHF** and **1000 CHF** for for-profit companies. 
 \n\nWhile participants are registered on a first come\, first serve basis\
 , exceptions may be made to ensure diversity and equity\, which may increa
 se the time before your registration is confirmed.\n\nApplications will cl
 ose on **15/10/2025** or as soon as the places will be filled up. Deadline
  for free-of-charge cancellation is **26/10/2025**. Cancellation after thi
 s date will not be reimbursed.\n\nYou will be informed by email of your re
 gistration confirmation. Upon reception of the confirmation email\, partic
 ipants will be asked to confirm attendance by paying the fees within 5 day
 s.\n\n\n# Venue and Time\n\nThis course will only be streamed. It will tak
 e place at four Wednesday afternoons from 13:00 - 17:00 CEST on:\n\n- 5 No
 vember \n- 12 November\n- 19 November\n- 26 November\n\nPrecise informatio
 n will regarding the communication platform will be provided to the partic
 ipants in due time.\n\n\n\n\n\n#  Additional information\n\n\nCoordination
 : Geert van Geest\, SIB Training group\n\nWe will recommend 0.5 ECTS credi
 ts 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 important deadlines usin
 g the form [here](https://lists.sib.swiss/mailman/listinfo/courses).\n\nPl
 ease note that participation in SIB courses is subject to our [general con
 ditions](https://www.sib.swiss/training/terms-and-conditions).\n\nSIB abid
 es by the [ELIXIR Code of Conduct](https://elixir-europe.org/events/code-o
 f-conduct). Participants of SIB courses are also required to abide by the 
 same code.\n\nFor more information\, please contact [training@sib.swiss](m
 ailto://training@sib.swiss).
SUMMARY:UNIX Shell Scripting in Life Sciences
URL;VALUE=URI:https://www.sib.swiss/training/course/20251105_ADVUN
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