clockSim: clockSim: Streamlined Simulation of Circadian Gene Networks

In clockSim: Streamlined Simulation of Circadian Gene Networks

clockSim: Streamlined Simulation of Circadian Gene Networks

Description

This package provides preconfigured circadian clock gene network simulation models based on the Odin simulation engine.

Details

The circadian clock is a foundational model for studying negative-positive feedback mechanisms in biology. The molecular clock—a cell-autonomous transcriptional-translational feedback loop—is one of the most well-characterized gene network oscillators.

Despite widespread interest in molecular clock research, numerical simulation of these systems remains inaccessible to many, if not most, wet-lab biologists. This gap has hindered the generation of novel hypotheses and efficient exploration of the clock’s parameter space.

'clockSim' addresses this challenge by providing a low-friction workflow for simulating molecular clocks, making in silico exploration accessible to a broader audience.

Please refer to the package vignettes on workflows provided by 'clockSim'.

The currently implemented models are based on the classical Leloup-Goldbeter PER-TIM feedback loop. Refer to Leloup and Goldbeter (1998) doi:10.1177/074873098128999934.

clockSim documentation built on April 11, 2025, 5:40 p.m.