BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling

Area of Science:

• Systems biology
• Synthetic biology
• Computational biology

Background:

• Understanding cellular signaling and regulatory networks is crucial for systems and synthetic biology.
• Investigating evolutionary processes that shape network structure and dynamics is challenging.
• Existing in silico evolution tools for network dynamics are limited.

Purpose of the Study:

• To introduce BioJazz, a novel tool for simulating the evolution of dynamic biochemical networks.
• To enable the study of evolutionary principles in biological network design.
• To facilitate the engineering of novel cellular networks.

Main Methods:

• BioJazz combines rule-based modeling with a genome-like encoding for network representation.
• The tool supports the evolution of cellular networks with unbounded complexity.
• Biologically realistic selective pressures can be implemented within BioJazz.

Main Results:

• BioJazz allows exploration of network architectures and dynamics for specific physiological functions.
• The tool demonstrates the feasibility of simulating evolutionary processes in biochemical networks.
• It provides insights into how evolutionary processes shape network properties.

Conclusions:

• BioJazz is a user-friendly, extendable, open-source tool for simulating the in silico evolution of dynamic biochemical networks.
• It overcomes limitations of previous tools by allowing for unbounded network complexity.
• The tool facilitates research in systems biology, synthetic biology, and evolutionary network design.