TinkerCell: modular CAD tool for synthetic biology

Area of Science:

• Synthetic biology
• Computational biology
• Bioengineering

Background:

• Synthetic biology integrates engineering and biology, necessitating computer-aided design (CAD) to connect computational models with biological data.
• CAD applications can streamline the design and construction of synthetic biological networks by enabling model building from biological parts and direct DNA sequence generation.

Purpose of the Study:

• To introduce TinkerCell, a novel CAD application developed as a visual modeling tool specifically for synthetic biology.
• To highlight TinkerCell's capabilities in supporting hierarchical biological parts, modular network construction, and integration with external analysis tools.

Main Methods:

• TinkerCell employs a visual modeling interface with a hierarchy of biological parts, each defined by attributes like sequence and rate constants.
• It supports modular network design, allowing the connection of interconnected modules with defined interfaces.
• The application integrates third-party C and Python programs through an extensive API for model analysis.

Main Results:

• TinkerCell provides a visual platform for constructing and analyzing synthetic biological networks.
• It supports a hierarchical structure for biological parts and enables the creation of modular networks.
• The tool facilitates the integration of external analysis tools via C and Python APIs.

Conclusions:

• TinkerCell's flexible framework is adaptable to the evolving field of synthetic biology, including new methods for part characterization and network analysis.
• It serves as a platform for testing various computational methods relevant to synthetic biology.
• The open-source nature and available resources (downloads, documentation, tutorials) promote its adoption and development.