# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "sRACIPE" in publications use:'
type: software
license: MIT
title: 'sRACIPE: Systems biology tool to simulate gene regulatory circuits'
version: 2.4.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.sRACIPE
- type: url
  value: https://vivekkohar.github.io/sRACIPE/
abstract: sRACIPE implements a randomization-based method for gene circuit modeling.
  It allows us to study the effect of both the gene expression noise and the parametric
  variation on any gene regulatory circuit (GRC) using only its topology, and simulates
  an ensemble of models with random kinetic parameters at multiple noise levels. Statistical
  analysis of the generated gene expressions reveals the basin of attraction and stability
  of various phenotypic states and their changes associated with intrinsic and extrinsic
  noises. sRACIPE provides a holistic picture to evaluate the effects of both the
  stochastic nature of cellular processes and the parametric variation.
authors:
- family-names: Lu
  given-names: Mingyang
  email: m.lu@northeastern.edu
  orcid: https://orcid.org/0000-0001-8158-0593
- family-names: Kohar
  given-names: Vivek
- family-names: Tillman
  given-names: Aidan
- family-names: Ramirez
  given-names: Daniel
preferred-citation:
  type: article
  title: Role of noise and parametric variation in the dynamics of gene regulatory
    circuits
  authors:
  - family-names: Kohar
    given-names: Vivek
  - family-names: Lu
    given-names: Mingyang
    email: m.lu@northeastern.edu
    orcid: https://orcid.org/0000-0001-8158-0593
  journal: npj Systems Biology and Applications
  year: '2018'
  volume: '4'
  url: https://www.nature.com/articles/s41540-018-0076-x
  start: '40'
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/lusystemsbio/sRACIPE
commit: b6f9b3e7978428733a44c16bfc775984b2ef910a
url: https://geneex.jax.org/
date-released: '2026-04-28'
contact:
- family-names: Lu
  given-names: Mingyang
  email: m.lu@northeastern.edu
  orcid: https://orcid.org/0000-0001-8158-0593
references:
- type: article
  title: 'sRACIPE 2.0: a systems biology circuit modeling toolkit for random circuit
    perturbation'
  authors:
  - family-names: Tillman
    given-names: Aidan
  - family-names: Ramirez
    given-names: Daniel
  - family-names: Lu
    given-names: Mingyang
  journal: Bioinformatics
  year: '2026'
  volume: '42'
  url: https://doi.org/10.1093/bioinformatics/btag019
  doi: 10.1093/bioinformatics/btag019