A workflow for the hybrid modelling and simulation of multi-timescale biological systems

Area of Science:

• Computational Biology
• Systems Biology
• Biochemical Engineering

Background:

• In-silico biological experimentation relies on model construction and simulation.
• Biological systems often involve reaction networks with multiple timescales (e.g., slow and fast).
• Hybrid simulation is a key technique for efficiently executing multi-timescale models.

Purpose of the Study:

• To present a methodology and workflow for constructing complex hybrid models.
• To integrate algorithms from hybrid simulation and Petri nets.
• To demonstrate efficient execution of multi-timescale hybrid models.

Main Methods:

• Utilizing coloured hybrid Petri nets for model construction.
• Developing a workflow integrating hybrid simulation and Petri net concepts.
• Constructing multi-timescale hybrid models.

Main Results:

• A novel methodology and workflow for creating smaller, more complicated hybrid models.
• Successful construction of multi-timescale hybrid models.
• Demonstration of efficient model execution using three advanced hybrid simulation algorithms.

Conclusions:

• The presented workflow facilitates the construction of sophisticated multi-timescale biological models.
• Hybrid Petri nets offer a powerful tool for in-silico biological experimentation.
• Advanced hybrid simulation algorithms enable efficient execution of complex biological models.