Libre Biotech User Manual
Comprehensive guide to using the Libre Biotech research data management platform.
What is Libre Biotech?
Libre Biotech is an open-source research infrastructure platform for the life sciences. It combines laboratory information management, protocol versioning, sequencing QC dashboards, analysis pipelines, and a genome browser into a single platform built on FAIR data principles.
The platform is designed for:
- Research groups managing genomics, transcriptomics, biodiversity, or environmental projects
- Core facilities tracking samples, sequencing runs, and analysis across multiple projects
- Institutions needing FAIR-compliant metadata capture with provenance tracking
- Community scientists who want accessible, professional-grade research data management
Platform components
| Component | What it does |
|---|---|
| ISA Framework | Structure research as Investigations, Studies, and Assays with ontology-annotated metadata |
| Processes & Samples | Track every step from sample collection through extraction, library prep, sequencing, and analysis |
| Protocol Library | Versioned, forkable SOPs with step-by-step instructions and community review |
| Sequencing QC | Dashboards for Illumina, Oxford Nanopore, and PacBio platforms with per-run quality metrics |
| Analysis Pipelines | Execute CWL workflows with full provenance tracking and RO-Crate packaging |
| Genome Browser | Integrated JBrowse 2 with custom tracks linked to analysis outputs |
| Collaboration | Groups, projects, tasks, reviews, comments, and share links |
| Training | Structured courses with modules and lessons |
| Community | User profiles, activity feeds, and public discovery pages |
How this manual is organised
| Section | For whom | Covers |
|---|---|---|
| Getting Started | New users | Registration, first project, navigation |
| Key Concepts | Everyone | ISA framework, FAIR principles, access control model |
| Research Data | Researchers | Creating and managing investigations, studies, processes, samples |
| Lab & Analysis | Lab staff, bioinformaticians | Protocols, pipelines, sequencing QC, storage |
| Collaboration | Teams | Groups, projects, tasks, training |
| Data & Compliance | Data managers, PIs | FAIR compliance, data export, search |
| Reference | Admins, developers | Administration, API documentation |
Open source
Libre Biotech is licensed under AGPL-3.0. The source code is freely available, and the platform can be self-hosted. Your data stays yours — full export in standard formats, no vendor lock-in.
Data sovereignty: All research data you create remains your intellectual property. You can export everything at any time in ISA-JSON, ISA-Tab, RO-Crate, or CSV format. See the Data Sovereignty Statement for full details.