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SUMMARY:Building and Using HPC-Compliant Snakemake Data Analysis Workflows
DTSTART:20261116T080000Z
DTEND:20261117T160000Z
DTSTAMP:20261022T110300Z
UID:indico-event-19049@indico.global
CONTACT:nhr-sw@csc.uni-frankfurt.de
DESCRIPTION:Speakers: Christian Meesters (Center for Scientific Computing\
 , Goethe University Frankfurt)\n\nOverview\nThis course equips participant
 s with the essential skills to design\, implement\, and run High-Performan
 ce Computing (HPC) compliant data analysis workflows using the Snakemake w
 orkflow management system. Through hands-on exercises and practical demons
 trations\, attendees will learn how to select\, execute\, and optimize the
  power of this workflow manager to utilize HPC resources effectively and e
 nsure reproducibility in their data analysis workflows. The Snakemake work
 flow system is widely used in bioinformatics\, experimental physics\, and 
 other data analysis fields.\nAgenda\n\nWorkflow Design and Implementation:
  Step-by-step instructions for designing and implementing HPC-compliant wo
 rkflows using Snakemake\, including best practices for parallelization and
  resource management.\nOptimizing Performance: Techniques for optimizing w
 orkflow performance on HPC clusters\, including resource allocation and av
 oiding I/O contention.\nEnsuring Reproducibility: Strategies for ensuring 
 reproducibility and scalability in data analysis workflows.\nCase Studies 
 and Practical Examples: Real-world case studies and practical examples dem
 onstrating the application of HPC-compliant Snakemake workflows in various
  data analysis scenarios.\nIntroduction to Snakemake and HPC: Overview of 
 the Snakemake workflow management system and the importance of HPC complia
 nce in data analysis workflows.\nSetting up your HPC Environment: Guidance
  on configuring Snakemake for HPC environments\, including considerations 
 for batch systems and job scheduling.\nAutomatic Software Deployment: Lear
 n about Snakemake's software support options.\nPublishing and registering 
 workflows with the Snakemake Workflow Catalogue for better visibility and 
 citation.\nQ&A and Troubleshooting: Opportunity for participants to ask qu
 estions\, seek clarification\, and troubleshoot challenges encountered dur
 ing the tutorial.\n\n \nThe course material (slides) will be made availab
 le to the class participants.\nLearning Outcomes\nBy the end of this tutor
 ial\, participants will:\n\nUnderstand the principles of HPC compliance in
  data analysis workflows.\nBe proficient in configuring Snakemake for HPC 
 environments and leveraging HPC resources effectively.\nBe able to design\
 , implement\, and optimize HPC-compliant data analysis workflows using Sna
 kemake.\nPossess the skills to optimize workflow performance\, ensure repr
 oducibility\, and troubleshoot common challenges in HPC environments.\nGai
 n insights from real-world case studies and practical examples to apply HP
 C-compliant Snakemake workflows in their research projects effectively.\n\
 nPrerequisites\n\nAbility to navigate the shell (bash) for basic file mani
 pulation and command execution.\nAbility to log in to remote servers via S
 SH (Secure Shell) for remote access\nFamiliarity with fundamental concepts
  of HPC\, including job scheduling\, parallel computing\, and resource all
 ocation\, is beneficial.\nBasic knowledge of the Python scripting language
  is beneficial\, including variables\, data structures\, control flow stat
 ements\, and functions.\n\n \nMinimum Enrolment: This course requires a m
 inimum of 6 participants to run. We reserve the right to cancel the course
  if this threshold is not met. In the event of a cancellation\, you will b
 e notified at least one week before the start date.\nLocation: Takes place
  at the campus Riedberg of Goethe University Frankfurt in room 01.120 of t
 he Physics Building\, Max-von-Laue Straße 1. Detailed travel directions w
 ill be provided to accepted participants in advance.\nEligibility: Exclusi
 ve to members of academic institutions. The organizer reserve the right to
  revoke non-eligible registrations!\nRegistration Fee: None (exclusive to 
 academic institution members)\nOrganization: Organized by the NHR@SW.\n\nh
 ttps://indico.global/event/19049/
LOCATION:01.120 (Frankfurt\, Riedberg\, Physik)
URL:https://indico.global/event/19049/
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