GitLab as Electronic Lab Notebook (ELN)

Overview

Value: This use case establishes GitLab as a secure, self-managed Electronic Lab Notebook (ELN) for laboratory environments. By leveraging GitLab Issues, Markdown templates, and QR-code– based automation, the solution enables standardized, version-controlled, and audit-ready experiment logging without the necessity of external ELN platforms. The approach improves traceability, compliance, and operational efficiency using existing GitLab infrastructure.

Problem: Appropriate tracking of consecutive and multiple repeated experiments following a device-specific procedure which supports for easy and anonymous probe handling within the experiment and their documentation.

Solution: GitLab is repurposed as an ELN by using issues as immutable experiment records, standardized markdown-based issue templates for protocols, and GitLab,s built-in features. A Python-based automation generates equipment-specific GitLab Issue URLs and encodes them into QR codes, allowing lab personnel to instantly create or access experiment logs directly from instruments using mobile devices or barcode scanners.

Who Benefits

When to Use

• When laboratory experiment documentation must be version-controlled and auditable.
• When institutions want a self-managed ELN without third-party SaaS dependencies.
• When experiment creation should be simplified via QR codes at lab instruments.

When Not to Use

• When regulatory frameworks mandate certified commercial ELN platforms.
• When offline-only experiment documentation is required.

Process

1. Pre-requisite step: define templates for the specific experiments.
2. Pre-requisite step: define labels for the various probes being used.
3. A Python script generates a GitLab Issue URL with a preloaded experiment template.
4. The URL is encoded into a QR code and attached to laboratory equipment.
5. A technician or researcher scans the QR code using a mobile device or scanner.
6. Each QR code scan triggers the creation of a new GitLab issue with a unique identifier, ensuring that every experiment is recorded as an independent.
7. The experiment is logged using pre-defined Markdown templates.
8. GitLab automatically tracks all changes, comments, and timestamps.

Requirements

Risks & Mitigations

• User resistance to replacing paper lab notebooks

  • Provide short training on QR-based ELN workflow
  • Offer parallel paper-to-digital transition period

• Improper access configuration leading to data exposure

  • Strict GitLab role definitions
  • Regular access reviews by QA/IT

• Template changes affecting historical consistency

  • Version all templates in Git
  • Restrict template changes via merge request reviews

Getting Started

"Prerequisites: GitLab access, basic Git knowledge, and Python installed for QR generation scripts."

1. Create a GitLab project to serve as the ELN repository
2. Define standardized Markdown-based issue templates
3. Configure access roles for researchers technicians, QA, and auditors
4. Generate QR codes linked to GitLab Issue URLs using Python scripts
5. Attach QR codes to laboratory instruments and begin logging

Resources

• GitLab Issues Documentation
• GitLab Access Control
• GitLab Markdown Guide

FAQ

Glossary

ELN

Electronic Lab Notebook used for recording laboratory experiments.

GitLab Issue

A GitLab object used here as a structured experiment log.

QR Code

Machine-readable code linking physical lab equipment to digital records.

GWP

Wissenschaftliche Praxis (Funding principles by DFG)