Foreword

This training aims at introducing the concepts at the core of LabID design, as well as teaching users how to use common and advanced features.

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

Summary

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	10 min	Go
2 - Creating workflows from local files	10 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