2026-08-13 –, Room 1
Hybrid and multiscale modeling gives rise to complex systems that are often difficult to simulate. Such models are integral to many areas of biology, where simple mechanisms can induce complex emergent phenomena across scales. We have developed Mermaid.jl, in which complex systems can be treated as components (models) and connections between them. We demonstrate the power of this approach through a range of examples, from the scale of single proteins to entire populations.
Mermaid.jl is a new package aimed at simplifying the simulation of hybrid (continuous and discrete) and multiscale systems. It uses a component-based architecture where modular components are stepped forwards in time and synchronized through variables passed along user defined inter-connections. Components are simulated using other packages and controlled and connected by Mermaid through a minimal interface. Mermaid already has implementations of this interface for many common modeling paradigms covering agent-based systems and differential equations. Additionally, Mermaid is designed to be highly user-extensible, allowing new packages to easily meet the Mermaid interface.
In this talk, we will present the core features of Mermaid.jl using several examples as a guide. This will include the simulation of an engineered genetic oscillator in a growing population of cells that combines agent-based modelling with an SDE of gene regulatory network function and ODE of cell growth. We end by comparing Mermaid.jl to other tools both inside and outside of the Julia ecosystem (e.g., Julia’s ModelingToolkit and Python’s Vivarium). We will demonstrate why these tools are limited for general hybrid and multiscale modeling, and the aspects of Julia that mean it could be a great language for these problems in future.
I am a mathematical biologist from the University of Bristol, UK. I have previously worked on efficient parameterisation of cardiac ion channel models, uncertainty quantification and models of blood coagulation. I currently work as a Postdoctoral Research Associate in Computation Biology within a synthetic biology group.