basicsynbio

basicsynbio facilitates design and instruction generation for DNA assemblies using the Biopart Assembly Standard for Idempotent Cloning (BASIC) to support modular, hierarchical synthetic biology workflows.

Key Features:

• Modular and idempotent assembly: Implements BASIC DNA assembly using modular parts and linkers to enable hierarchical, idempotent assembly workflows.
• Error handling and export: Incorporates exception handling for common assembly-design errors and exports sequence data and instructions for manual or acoustic liquid-handling platforms.
• BasicBuild Open Standard integration: Parses the BasicBuild Open Standard and serializes instruction sets in JavaScript Object Notation (JSON) for bespoke workflows.
• Compatibility with established collections and methods: Demonstrates assembly using Standard European Vector Architecture (SEVA) sequences and produces vectors compatible with both BASIC and Golden Gate assembly using BsaI, including varied antibiotic resistance markers and origins of replication.
• Programmatic API for parts and linkers: Exposes BASIC parts, linkers, and additional collections via an API for programmatic construct design.

Scientific Applications:

• Pathway engineering: Enables assembly of multi-part constructs for metabolic and biosynthetic pathway reconstruction.
• RBS tuning: Supports design of constructs for ribosome binding site (RBS) variation to modulate gene expression.
• Fusion protein engineering: Facilitates design of fusion proteins by combining modular parts and linkers.
• Multiplexed guide RNA expression: Enables construction of arrays for multiplexed guide RNA expression to support genome editing experiments.
• Iterative Design-Build-Test-Learn cycles: Supports iterative synthetic biology workflows through programmatic design, export, and instruction generation.

Methodology:

Implemented as a Python package that constructs hierarchical BASIC assemblies using modular parts and linkers, parses the BasicBuild Open Standard, serializes instructions to JSON, handles common design exceptions, and exports sequence data and liquid-handling instructions.