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.

While a LabID instance is available to all EMBL researchers, the platform is open-source and can be deployed at other institutes.

About the workshop

This one and a half 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 is this workshop for ?

The event is open to both EMBL-affiliated and external participants, and will be primarily happening in-person at the EMBL Heidelberg.

Whether you are new to LabID, or already use some of its functionality, this workshop gives you the opportunity to expand your knowledge of LabID, or become more familiar with its concepts.
We also encourage computational scientists and data-stewards to join !

Participation is limited to 20 participants on-site on a first-come first-served basis.

Prerequisites

Please bring your laptop, 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 (09:00 – 12:30)

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

Afternoon (13:30 – 18:00)

• 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