Part 3: Software Environments, Containers, and Reproducibility

Workshop Details

Managing software versions, packages, and dependencies on Quest can be challenging. These challenges are multiplied when working with collaborators or sharing your workflow with others who want to reproduce it. Learn how to use environments, containers, and workflow management systems to ensure your research produces consistent results over timeThese challenges are multiplied when working with collaborators or trying to share your workflow with others who want to reproduce it.  Learn how to use environments, containers, and workflow management systems to ensure your research produces consistent results overtime and can be reproduced by others. 

Prerequisites: This workshop is designed for those who have attended Part 1 of Research Computing Basics and Beyond, or who already know how to transfer data to and from Quest, navigate Quest from the command line, and submit batch jobs.   

Attendees will learn how to: 

• Create a virtual environment to manage software packages and versions 

• Set up a virtual environment optimized to use Quest’s GPU resources 

• Use and deploy Docker/Singularity containers to ensure a consistent computing environment across people and even different computing systems 

• Use GitHub to support setting up and managing containers 

• Use Nextflow to manage multipart computational workflows, including popular bioinformatic pipelines from nf-core 

• Develop a reproducible workflow that will support both you and others in achieving consistent results 

Event Details

All Research Computing Basics and Beyond workshops are held in person; there is no hybrid option or recording available. These are interactive, hands-on workshops; participants are required to bring their laptop and charger.

Lunch breaks will be provided; participants are responsible for their own lunch.

Attendees

Members of the Northwestern community with an active Northwestern NetID as of the date of the workshop are eligible to attend. Registrations made by those without an active NetID may be cancelled. If you will be at Northwestern this summer, but do not yet have a NetID, please register but email nuit_rcds@northwestern.edu to let us know of the situation.

Refunds and Cancellations

Research Computing Basics and Beyond refunds (minus Eventbrite and credit card fees) will be given to cancellations seven (7) days before the event.

Northwestern registrants needing to cancel with fewer than seven (7) days notice can contact nuit_rcds@northwestern.edu for possible refunds.