LabID PROV Workshop — September 2026¶
This 1.5-day workshop was organised in September 2026 as part of the LabID-PROV project, funded by the EU OSCARS research consortium.
The workshop included talks and hands-on sessions, following tutorials featured on this documentation website. Most talks were recorded and are linked below. The tutorials are also linked and most of them can be followed using the LabID demo instance (labid-demo.embl.de). Note that a dedicated training instance of LabID was deployed for this training, which might slightly defer from the public demo instance.
Workshop details — dates, format and accessing the training environment
The workshop covers general data management use cases (sample creation and annotation, integration with the embedded ELN, data registration) to the most recent features on workflow management and provenance (workflow import and creation, workflow-run registration, Galaxy integration, RO-Crate export). Data publication will also be demonstrated.
- Dates: Monday 28 September 2026, 13:00 → Tuesday 29 September 2026, 17:00
- Format: 1.5 days — presentations, hands-on sessions and user-community talks
Follow the hands-on sessions using a training instance of LabID (https://labid-training.embl.de). Logging in as a trainee user after booking a user account in the shared ggsheet (link communicated during the training).
We advise against using a production instance as this will greatly pollute your database.
Use case : spatial transcriptomics
The practical hands-ons in this workshop present a fictional scientific use case involving imaging and sequencing, using samples taken from a common specimen. These hands-on follow on from one another in a logical sequence, so it is important to complete them in the order suggested. Here is a visual representation of the data-provenance recorded in LabID at the end of the training (a similar representation is generated in LabID by the built-in Lineage Graph viewer).
Day 1 — Monday 28 September 2026¶
All times are in CEST and are approximate. The schedule may change depending on how long the hands-on sessions take.
| Time | Title | Presenter / Details | Duration | Link | ||||
|---|---|---|---|---|---|---|---|---|
| 13:00 | Welcome | 10 min | ||||||
| 13:10 | Data Management, Integration and FAIRification with LabID (Talk) | Charles Girardot | 30 min | |||||
| 13:40 | Hands-on session 1 — Derive Sample from Specimen with ELN | Charles Girardot | 1h20 | Go | ||||
| 15:00 | User talk - Using LabID for lab management (ELN, protocols...) | Inés Romero Brey | 15 min | |||||
| 15:15 — Coffee break (20 min) | ||||||||
| 15:35 | Q&A — previous hands-on | All trainers | 5 min | |||||
| 15:40 | Common Features & Batch operations (Talk) | Charles Girardot | 20 min | |||||
| 16:00 | Register image data (mouse brain images) | Laurent Thomas | 40 min | Go | ||||
| 16:40 | Data Storage Organization in LabID (Talk) | Charles Girardot | 10 min | |||||
| 16:50 | Register sequencing data | Charles Girardot | 50 min | Go | ||||
| 17:40 | Q&A — previous hands-on & Wrap-up | All trainers | 15 min | |||||
| 18:00 | Social event - Pizza and drinks at ATC Rooftop | |||||||
Day 2 — Tuesday 29 September 2026¶
All times are in CEST and are approximate. The schedule may change depending on how long the hands-on sessions take.
| Time | Title | Presenter / Details | Duration | Link | ||||
|---|---|---|---|---|---|---|---|---|
| 09:00 | Recap of Day 1 | 10 min | ||||||
| 09:10 | Workflow Integration in LabID | Laurent Thomas | 15 min | |||||
| 09:25 | Hands-on 1 - Importing workflows from repositories (ex: Galaxy) | Laurent Thomas | 10 min | Go | ||||
| 09:35 | Hands-on 2 - Creating workflows from local files (e.g. notebooks) | Laurent Thomas | 25 min | Go | ||||
| 10:00 | User talk - Using LabID for sequencing data management | Cyril Cros | 15 min | |||||
| 10:15 — Break (15 min) | ||||||||
| 10:30 | Registering workflow run - image-conversion (steps 1-5) | Laurent Thomas | 40min | Go | ||||
| 11:10 | Integration capabilities and data flows with LabID (presentation) | Charles Girardot | 15 min | |||||
| 11:25 | Importing workflows and workflow runs from Galaxy | Laurent Thomas | 35 min | Go | ||||
| 12:00 | User talk - LabID at ETH Zürich / FMI | Elisa Kreibich and Gustavo Q. G. de Medeiros | 15 min | |||||
| 12:15 — Lunch break (with coffee) | ||||||||
| 14:00 | Data export and submission | Charles Girardot | 30 min | |||||
| 14:30 | Intro to RO-Crate and integration in LabID | Laurent Thomas | 15 min | |||||
| 14:45 | Hands-on — Workflow and Workflow Run RO-Crates (export and exploration) | Laurent Thomas | 40 min | Go | ||||
| 15:25 — Coffee break (20 min) | ||||||||
| 15:45 | LabID customization (custom annotation types, assay...) | Nayeem Reza | 20 min | |||||
| 16:05 | Wrap-up & feedback | open discussion until 17:00 | ||||||