What is LabID ?

LabID is an all-in-one data management platform for life-science research, designed to help researchers, labs and facilities organise their data, and keep track of its experimental provenance. LabID provides an inventory, sample and data-management, an electronic lab notebook and an integration with workflow engines like Galaxy.

LabID is open-source, and primarily developed at the EMBL. A central installation is currently deployed across the EMBL sites, and a few other institutes and research groups also started deploying their own instance.

About the workshop

Participation to the event is free and open to both EMBL-affiliated and external participants.
The workshop will take place at EMBL Heidelberg, from Monday Sept 28th after lunch to Tuesday evening, and is offered in a hybrid format.
On-site participation is limited to 20 participants.

This 1.5-day workshop will start with a general introduction about data-management with LabID, covering the different concepts (study, assay, sample), illustrated with hands-on tutorials and concrete use-cases.

For the second day, we will present the newer workflow integration of LabID, and how it can be used to document the provenance of derived datasets, such as ones generated by workflows or simpler scripts. This second part will be illustrated with sequencing workflows (e.g from Nextflow) and/or an image-conversion workflow (conversion of microscopy images to OME-Zarr).

Who should attend ?

Whether you’re new to LabID or already have access to an installation and use some of its features, this workshop will help you become more comfortable with LabID’s concepts and get the most out of it.
All user profiles are welcome: wet lab researchers, computational scientists, data stewards, lab managers, and system admins!

Prerequisites

Please bring your laptop !

For WIFI, eduroam is available on-site for external participants (please check your institute guideline before coming), as well as a guest wifi.

Feel free to create an account at dev.workflowhub.eu before the workshop, this will be used to illustrate the direct publication of workflows from LabID.

Agenda (draft)

Monday Sept 28th – afternoon (13:00 – 18:00)

• welcome remarks
• introduction to LabID (lab/biomaterial management, electronic lab notebook, data-management)
• concepts of dataset, study, assay
• hands-on raw data-registration

Monday evening

Social event (details will follow)

Tuesday Sept 29th (09:00 – 18:00)

Morning

• LabID workflow integration : introduction
• concepts of workflows, versions and runs
• import of workflows from git, galaxy, and local files

Afternoon

• registering workflow runs in LabID (imaging and/or sequencing)
• export of workflows and workflow runs as RO-Crates
• real-life examples / S3 integration
• Q&A Wrap-up

If you have any further questions, feel free to contact modis@embl.de.

Bookings