GeneRegulatorySystems.jl

This software constructs and orchestrates the simulation of single-cell gene regulatory models.

Overview

The package contains components to construct complex models of single-cell gene regulation from templates and can coordinate reproducible simulation through a flexible scheduling mechanism and output format. The core regulation models are currently defined using Catalyst.jl and simulated via JumpProcesses.jl, allowing them to be treated in isolation with various tools from the SciML ecosystem. Scheduling supports various forms of instant adjustment and fine-grained output control.

Features include:

• Construction of Catalyst.jl ReactionSystem-based gene regulation models using a simple JSON-based template language.
• Simulation using exact stochastic methods from JumpProcesses.jl.
• Experiment scheduling mechanism that supports complex observation models, seed control and simulation branching, as well as persistent and transient interventions (including periodic interventions).
• Export to counts matrices for downstream applications.

Usage

The package can be used either as a standalone application or as a library.

• The primary use case is to use the included command line tools to run prepared simulation experiments and potentially to export the results to (wide-format) molecular counts data. See Getting started for instructions and Results format for a description of the native on-disk format.

• The advanced use case is to import and use this package in a Julia session to access the produced (mostly SciML-based) models, either because more control over the simulation is required or to enable static analysis. This is described in Usage as a library.

Both variants require a working installation of Julia ≥ v1.10. This package is currently not registered.