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

Aidan Tillman, Daniel Ramirez, Mingyang Lu

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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0 citing papers in PubMed.

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5 · Who and what money

Authors and funding

3 authors.

Aidan TillmanDepartment of Bioengineering, Northeastern University, Boston, MA 02115, United States.ORCID 0009-0001-3860-9650

Daniel RamirezDepartment of Bioengineering, Northeastern University, Boston, MA 02115, United States.ORCID 0000-0003-3258-834X

Mingyang LuDepartment of Bioengineering, Northeastern University, Boston, MA 02115, United States.ORCID 0000-0001-8158-0593

Funding

New Computational Systems Biology Methods for Modeling Gene Regulatory CircuitsR35GM128717 · NIGMS · NORTHEASTERN UNIVERSITY · PI Mingyang Lu · 2018 to 2026

$3.3M

Center for Theoretical Biological Physics at Northeastern UniversityNational Institute of General Medical Sciences of the National Institutes of Health R35GM128717NIGMS NIH HHS R35 GM128717Northeastern UniversityNortheastern University Bioengineering Department Dean's FellowshipOn-Ramp into Research Endeavors (CORE)

6 · The paper itself

Abstract

summaryThe 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. AVAILABILITY AND IMPLEMENTATION: 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.

Indexed as

Gene Regulatory NetworksSoftwareSystems BiologyAlgorithms

Identifiers

PMID41555502

DOI10.1093/bioinformatics/btag019

PMCPMC12866642

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LicenceCC BY

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.