LabxDB

LabxDB manages centralized laboratory and high-throughput sequencing (HTS) data, providing structured storage and programmatic access to support bioinformatics workflows.

Key Features:

• Centralized Data Management: Provides a unified platform for organizing lab collections and genomic sequencing datasets to enable multi-user data sharing.
• Pre-configured Databases: Includes ready-to-use databases for mutant and plasmid collections and for purchase-tracking, deployable in cloud environments.
• HTS Annotation Database (LabxDB seq): Implements a specialized HTS annotation database for hierarchical storage and management of high-throughput sequencing sample annotations.
• Hierarchical Sample Annotation Model: Organizes annotations across multiple levels from projects to individual sequencing runs.
• REST API: Exposes a REST API for programmatic access and integration into bioinformatics pipelines.
• HTS Data Import: Supports importing HTS data from local facilities and public resources.
• Modular Framework: Provides a modular framework that can be adapted to build new database interfaces tailored to specific research needs.
• PostgreSQL Backend: Uses PostgreSQL as the underlying database system for robust multi-user data storage.

Scientific Applications:

• HTS Annotation and Management: Organizing and annotating high-throughput sequencing datasets across projects, samples, and runs.
• Integration into Bioinformatics Pipelines: Enabling incorporation of HTS metadata and sample annotations into bioinformatics pipelines via the REST API.
• Laboratory Inventory and Collections: Managing mutant and plasmid collections and tracking purchases within laboratory databases.
• Data Lifecycle Tracking: Tracking HTS datasets through production, analysis, and publication stages.

Methodology:

LabxDB uses PostgreSQL as its underlying database, implements hierarchical annotation storage for HTS data, exposes a REST API for programmatic access, and supports importing HTS data from local facilities and public resources.