Bioparts

Bioparts provides centralized capture, storage, and sharing of DNA parts metadata to support synthetic biology research by enabling distributed ICE registries to connect, query, and exchange entries.

Key Features:

• Web of Registries Concept: Implements the Web of Registries on the ICE platform to connect standalone ICE installations into a distributed parts database enabling cross-registry queries of plasmids, strains, DNA parts, plant seeds, and proteins.
• Data Transfer and Accessibility: Supports transferring entries between ICE registries and marking entries as public to enable cross-institutional data sharing.
• Comprehensive Search Functionality: Integrates sequence-based search capabilities including BLAST and federated queries across sources such as NCBI, iGEM, SynBioHub, Addgene, and ICE registries.
• REST API Integration: Exposes a REST API for programmatic access to search, retrieve, and exchange parts metadata.

Scientific Applications:

• Parts discovery: Locate and retrieve plasmids, strains, DNA parts, plant seeds, and protein entries across multiple registries and databases.
• Genetic construct design: Support designing new genetic constructs by providing access to annotated DNA parts and sequence search (BLAST) results.
• Comparative analysis and annotation: Analyze and compare existing biological systems using aggregated metadata from ICE registries and external sources such as NCBI, iGEM, SynBioHub, and Addgene.

Methodology:

Captures detailed metadata for biological parts and stores it in a distributed database via the Web of Registries on ICE, implements BLAST-based sequence search and federated queries across NCBI, iGEM, SynBioHub, Addgene, and ICE registries, and exposes a REST API for programmatic access.