Features - BioMiner Indexd

Core Features

Built for modern biomedical data management

Global Unique Identifiers

Generate and manage globally unique identifiers for each data file with comprehensive metadata tracking.

UUID-based file identification
MD5 checksum verification
Comprehensive metadata storage
DOI number integration

File Location Tracking

Track file locations across multiple repositories with automatic synchronization and status monitoring.

Multi-repository support (OSS, S3, GSA, NODE, SRA, ENA)
Automatic location synchronization
Repository-specific metadata
Download link management

Multi-Version Management

Manage different versions of files with Base UUID indexing for comprehensive version control.

Base UUID for version grouping
Historical version tracking
Pipeline analysis support
Version comparison tools

Advanced Database Support

Flexible database configuration supporting both remote and local PostgreSQL deployments.

Remote PostgreSQL mode (production)
Local PostgreSQL mode (development)
Automatic schema management
High-performance queries

Technical Architecture

Built with modern technologies for reliability and performance

Rust Backend

High-performance, memory-safe backend built with Rust for optimal performance and reliability.

PostgreSQL

Robust relational database for storing metadata, file information, and indexing data with ACID compliance.

React Frontend

Modern web interface built with React and Ant Design for intuitive data exploration and management.

Quick Start Guide

Get up and running in minutes

1

Download BioMiner Indexd

Download the latest release from our GitHub repository:

                                    # Download from GitHub releases

                                    wget https://github.com/yjcyxky/biominer-indexd/releases/latest/download/biominer-indexd

2

Install PostgreSQL

Install PostgreSQL (Recommended version: 10.x or higher):

                                    # Ubuntu/Debian

                                    sudo apt-get install postgresql postgresql-contrib

                                    # macOS

                                    brew install postgresql

3

Configure Environment

Set up environment variables:

                                    # For remote PostgreSQL

                                    export DATABASE_URL=postgres://user:password@host:5432/biominer_indexd

                                    export BIOMIER_REGISTRY_ID=your-registry-id

                                    # For local PostgreSQL

                                    export BIOMIER_REGISTRY_ID=your-registry-id

4

Start the Service

Launch BioMiner Indexd:

                                    # Remote PostgreSQL mode

                                    ./biominer-indexd --host 0.0.0.0 --port 3000

                                    # Local PostgreSQL mode

                                    ./biominer-indexd --local-postgres --host 0.0.0.0 --port 3000

API Features

RESTful API for seamless integration

File Registration

Register new files with metadata and generate unique identifiers.

POST /api/files

File Lookup

Search for files by UUID, MD5, or other metadata criteria.

GET /api/files/{uuid}

Bulk Operations

Perform bulk file operations and batch downloads.

POST /api/files/bulk

Status Tracking

Track file status across multiple repositories.

GET /api/files/{uuid}/status