Simulating gene regulatory systems
Events / Oxford Seminar
One approach to describing gene regulation is to frame relevant molecular species and their interactions in terms of chemical reaction networks. The system’s dynamics are then given at the chosen level of granularity by a chemical master equation, which admits arbitrary non-linearity and feedback. Their study must therefore typically resort to simulation.
Our software package GeneRegulatorySystems.jl builds on Catalyst.jl, JumpProcesses.jl and other SciML components to orchestrate complex simulation experiments. We have used this framework to reproduce small-scale behavior known from the literature, to assemble simple components into larger systems, and to generate random systems from specific network models. This toolset enables exact trajectory samples from single-cell gene regulatory systems of up to tens of thousands of genes. The package also includes a flexible scheduling mechanism that allows modeling various experimental setups including parameter sweeps, interventions, simulation branching and non-trivial observation models.
In this talk, I will describe our modeling approach and software, the construction and simulation of concrete gene regulatory systems, the underlying regulation model, as well as the templating and scheduling mini-DSL.
This is joint work with David Jordan, Ștefan Manolache and Hajk-Georg Drost.
Paper preprint: https://www.biorxiv.org/content/10.64898/2026.11.01.763459v1 Package: https://github.com/drostlab/GeneRegulatorySystems.jl/ Documentation: https://lmshk.github.io/GeneRegulatorySystems.jl/