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SUMMARY:Designing Reproducible Workflows Using Snakemake
DTSTART;TZID=Europe/London:20260603T110000
DTEND;TZID=Europe/London:20260603T120000
DTSTAMP:20260527T025524Z
UID:5efb3f5c-4724-f111-8341-7ced8d99a758
CREATED:20260320T102720Z
DESCRIPTION:High-throughput technologies such as RNA sequencing—at both 
 bulk and single-cell levels—generate large volumes of complex data acros
 s many samples. Ensuring that these analyses are reproducible\, scalable\,
  and portable is a major challenge in modern bioinformatics.\n\nThis hands
 -on training course introduces participants to the principles and practica
 l implementation of reproducible computational workflows using Snakemake\,
  Conda\, and Docker. Participants will learn how to design structured pipe
 lines\, manage software dependencies\, and containerize analyses to ensure
  portability across computing environments.\n\nThis session will cover:\n1
 -Reproducibility Challenges in Bioinformatics\nCommon issues in managing s
 oftware dependencies and scaling analyses across multiple samples.\n\n2-In
 troduction to Workflow Management with Snakemake\nRules\, dependencies\, d
 ry runs\, and execution of a simple reproducible pipeline.\n\n3-Environmen
 t Management with Conda\nCreating isolated environments and integrating th
 em directly into Snakemake workflows using --use-conda.\n\n4-Containerizat
 ion Concepts with Docker\nBasic principles of Docker and how containers im
 prove portability and reproducibility.\n\n5-Combining Snakemake\, Conda\, 
 and Containers\nOverview of how these tools work together in modern bioinf
 ormatics pipelines.\n\nPre requisites: \nFamiliary with command line termi
 nal \n\nIntended audience: Anyone interested in performing bioinformatic a
 nalysis\n\nParticipants will need:  \nBring your own computer\nInstall doc
 ker\nInstall Visual Code IDE\n\nPre-Course Preparation: \nDocker\, Visual 
 Code \n\nDuration: presentation and practical workshop.
LAST-MODIFIED:20260320T130653Z
LOCATION:Big Data Institute - Seminar room 1\, Seminar room 1 Big Data Ins
 titute Old Road Campus Oxford Oxfordshire OX3 7LF United Kingdom
SPEAKER:Dr Andre Aquime Goncalves (Department of Paediatrics)
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