# sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation

## TL;DR

sRACIPE 2.0 is an updated toolkit for modeling gene regulatory circuits using random parameter simulations to study biological systems.

## Contribution

sRACIPE 2.0 introduces new features for modeling perturbation, extrinsic signaling, and time-corrected noise in gene regulatory circuits.

## Key findings

- sRACIPE 2.0 supports diverse interaction types in gene regulatory circuits using deterministic and stochastic simulations.
- The update includes a new diagnostic tool to ensure accurate simulations of biological systems.
- The toolkit is now available on GitHub and Bioconductor for broader use in systems biology.

## Abstract

The Random Circuit Perturbation (RACIPE) algorithm enables the exploration of the dynamical behaviors of gene regulatory circuits (GRCs) by simulating an ensemble of differential equation models via randomization of kinetic parameters. Here, we release sRACIPE 2.0, a major update to the R/Bioconductor package, as a unified platform for modeling GRCs with diverse interaction types using both deterministic and stochastic simulations. The update also introduces new features for modeling perturbation, extrinsic signaling and time-corrected noise, and a new diagnostic tool to ensure proper simulations. We hope that this release will serve as a versatile modeling toolkit for the systems biology community.

The package is available on GitHub at https://github.com/lusystemsbio/sRACIPE under the MIT license. It is also available on Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/sRACIPE.html.