sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit perturbation.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41555502.
- Also identified by DOI 10.1093/bioinformatics/btag019 and PMC identifier 12866642.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- Systems Biology
- Software
- Gene Regulatory Networks