Documentation

Group management, user permissions, pipeline execution, JBrowse genome browser, API usage, advanced search, and administrative features for power users. [Preview content available - full course under development]

eDNA metabarcoding, specimen collection protocols, chain of custody tracking, and public data deposition. For museums, conservation groups, and field programs.

Dashboard setup, client reporting, quality control workflows, and onboarding delegation. For university core facilities and shared platforms.

Hands-on workshop transforming research projects from spreadsheets to FAIR science. Learn the ISA framework, metadata standards, provenance tracking, and export strategies.

Complete workflow from sample collection to publication. QC dashboard interpretation, CWL pipeline management, and JBrowse genome browser usage.

Complete beginner guide to the platform. Account setup, first investigation, sample upload, basic navigation, and understanding the interface. Perfect for new users. [Preview content available - full course under development]

Deep dive into Investigations, Studies, and Processes. How to structure research projects, sample lineage, metadata standards, and data organization best practices. [Preview content available - full course under development]

Create reproducible, shareable protocols using structured formats. Equipment & materials catalogs, version control, and collaborative improvement workflows.

Navigate the protocol library, follow procedures, create protocols, and interpret QC dashboards (IlluminaQC, NanoporeQC, PacBioQC). Quality control workflows. [Preview content available - full course under development]

Master sample tracking, batch operations, file attachments, process chains, provenance tracking, and metadata entry. Advanced data management workflows. [Preview content available - full course under development]

Technical guide for deploying Libre Biotech on your own infrastructure. Installation, configuration, administration, backups, and troubleshooting. [Preview content available - full course under development]

Getting Started

• Create or join a Group to collaborate with your team
• Start an Investigation to organize your research project
• Add Studies under an investigation for different experimental arms
• Create Processes (labbook entries) to record your bench work

ISA Framework

• Investigation → top-level project container
• Study → experimental design within an investigation
• Assay / Process → individual lab procedures and data collection
• Sample → biological or chemical material tracked through processes

Process Categories

• Sample Preparation — extractions, library preps, pooling
• Measurement — Fragment Analyzer, qPCR, spectrophotometry
• Sequencing — sequencing submissions linked to QC runs
• Data Transformation — computational analysis linked to pipelines

Collaboration

• Groups control access — members see shared investigations and processes
• Comments on processes and investigations for discussion
• Reviews — request peer review and approval for processes
• Sharing — create external links for collaborators outside the system