Using containers in bioinformatics
Organizer: Australian BioCommons
Host institution: Australian Biocommons
Start: Thursday, 25 March 2021 @ 12:30
End: Friday, 26 March 2021 @ 16:00
Contact: Melissa Burke: firstname.lastname@example.orgDescription:
Are you wondering how your research could benefit from workflow containerisation?
Containers enable you to package up an application and its dependencies and encourage reproducibility, portability and shareability of computational workflows. This workshop explores the merits, advantages and limitations of applying containers in bioinformatics.
During the workshop you will:
learn and practice the basics of building, deploying and running applications in containers
explore real use cases related to biology
discuss tips and best practices, and have your questions answered.
This workshop will be delivered online through a combination of presentations, demonstrations and hands-on interactive exercises supported by containers experts. On day 1 you will learn new skills through undertaking practical exercises and on day 2 you can bring your own pipeline to get advice and tips in a small group setting.
By the end of the workshop you should be able to:
Identify when you would benefit from using containers in your workflow
Download container images and run commands from inside a container using Singularity
Identify popular image registries
Discuss the pros & cons of building with Singularity vs Docker
Describe the basic syntax of a Dockerfile
Build and share an image with Docker
Convert a Docker image into the Singularity format
Lead trainer: TBC
Date/time: 12:30pm - 4:00pm AEDT/ 11:30am - 3:00pm AEST/ 12:00pm - 3:30pm ACDT / 9:30am - 1:00pm AWST Thursday 25 - Friday 26 March 2021
Who the workshop is for
Basic familiarity with UNIX shell concepts and command line interactions are required. Participants do not need any previous experience with containers.
This workshop is open to staff and students from Australian universities and research institutes.
How to apply
The workshop is free but participation is subject to application with selection.
Please note that applications that do not nominate an Australian institute and do not provide an appropriate institutional email address will not be able to take part.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 19 March 2021. Participants will be provided with a Zoom meeting link closer to the date.
Please complete the application form if you are interested in attending this workshop.
Applications close 5pm AEDT Monday 15 March 2021.
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Keywords: Workflows, Containers