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Past Trainings

This page archives the content of previous LabID training sessions. For the current workshop, see the LabID PROV Workshop — September 2026 page.

Use a training instance

Follow this training using a training instance of LabID ( https://labid-demo.embl.de ) logging in as a trainee user (trainee1..100 e.g. trainee1), and the following password: 123456.

We advise against using a production instance as this will greatly pollute your database

2022-09 Training

Electronic Lab Notebook (ELN) and Lab Collections

Title Topics Duration Link
Overview Inventory, Sample & Data Management, Concepts 8min
Electronic Lab Notebook (ELN)
Presentation
1 - Explore Lab Notes Create a note & explore functionalities 25min
Go
2 - Explore Protocols Create a protocol & derive a lab note 15min
Go
3 - Explore Permissions & Lifecycle Understand the different status of an experiment 10min
Go
Lab Collection Management
Presentation Consumable, Equipment & Storage Equipment
1 - Create, Browse and Edit Items Create collection items & explore functionalities 45min
Go
2 - Batch Operations Batch create, edit and delete items 30min
Go

Sample Management

Title Topics Duration Link
Presentation
1 - Creation (and Lineage) 25min
Go
2 - Sample Editor 30min
Go
3 - Protocol List Templates 15min
Go
4 - Batch Creation 20min Go
5 - Sample Merging 15min Go

Dataset Management

Title Topics Duration Link
Dataset & Assay Management
Presentation Assay, raw datasets
1 - Registering Raw Datasets 101 (Imaging) Imaging data, dataset loader, basics 30min
Go
Presentation Derived datasets
2 - Registering Raw Datasets (Sequencing) Paired-end sequencing data, dataset builder 40min
Go
3 - Post register operations Renaming, batch edition, list view context 20min Go
4 - Registering managed raw datasets (Sequencing) Managed raw datasets, Genecore 20min
Go

Working with Galaxy

Title Topics Duration Link
Setup and data-Syncing Syncing data to a Galaxy instance for analysis 40min GO
Importing Galaxy workflow invocations Import a Galaxy workflow invocation as a workflow run 20min GO

Workflow Management

Title Duration Link
Overview of the workflow integration 30 min
1 - Importing workflows 25 min Go
2 - Creating workflows from local files 20 min Go
3 - Export workflows to WorkflowHub 15 min Go

Register workflow runs

Here you can choose one of 2 parallel tracks, both covering the registration of workflow runs from the UI and from the CLI, but using different use cases : sequencing using a Nextflow demo workflow, and imaging with an image-conversion workflow.

  • track sequencing
Title Duration Link
1 - Register a workflow run (Nextflow) via the web interface 20 min Go
2 - Executing a Nextflow workflow and register it with the CLI 50 min Go
  • track imaging
Title Duration Link
1 - Registering an image-conversion run via the web interface 25 min Go
2 - Execute an image-conversion run and register it with the CLI 50 min Go

Command Line Interface (CLI)

Title Topics Duration Link
1 - CLI - Getting Started Setup, Get data 15min Go
2 - CLI - Features Export Study and call for collaborations 15min Go
2 - CLI - Register workflow runs Execution of example workflows and registration 50min Go