R/data.R

In lusystemsbio/sRACIPE: Systems biology tool to simulate gene regulatory circuits

#' @title A toggle switch circuit for demonstrations
#' @description This data contains the topology of a
#' circuit with two genes A and B both of which inhibit each
#' other and have self activations. The interactions are transcription factor
#' interactions. For further details,
#' see Kohar, V. and Lu, M., Role of noise and parametric
#' variation in the dynamics of gene regulatory circuits,
#' npj Systems Biology and Applications 4, Article number: 40 (2018)
#' @format A data frame with 4 rows and 3 variables
"demoCircuit"

#' @title Five coupled toggle switches
#' @description This data contains the topology of a
#' circuit with ten genes A1...A5 and B1...B5.
#' Genes with different alphabet inhibit each other
#' whereas genes from different groups activate the other.
#' For further details,
#' see Kohar, V. and Lu, M., Role of noise and parametric
#' variation in the dynamics of gene regulatory circuits,
#' npj Systems Biology and Applications 4, Article number: 40 (2018)
#' @format A data frame with 18 rows and 3 variables
"CoupledToggleSwitchSA"

#' @title A circuit for epithelial to mesenchymal transition
#' @description This data contains the topology of a
#' circuit with sixteen genes invovled in EMT.
#' For further details,
#' see Kohar, V. and Lu, M., Role of noise and parametric
#' variation in the dynamics of gene regulatory circuits,
#' npj Systems Biology and Applications 4, Article number: 40 (2018)
#' @format A data frame with 59 rows and 3 variables
"EMT1"

#' @title A circuit for epithelial to mesenchymal transition
#' including microRNAs
#' @description This data contains the topology of a
#' circuit with twenty two nodes including
#' micro RNAs invovled in EMT.
#' For further details,
#' see Huang et al.,Interrogating the topological robustness
#' of gene regulatory circuits by randomization,
#' PLoS computational biology 13 (3), e1005456
#' @format A data frame with 82 rows and 3 variables
"EMT2"

#' @title Configuration Data
#' @description It contains simulation parameters
#' like integration method
#' (stepper) and other lists or vectors like simParams,
#' stochParams, hyperParams, options, thresholds etc.
#' The list simParams contains values for parameters like the
#' number of models (numModels), number of convergence iterations to run for
#' simulations with convergence tests (numConvergenceIter),
#' simulation time (simulationTime), step size for simulations
#' (integrateStepSize), when to start recording the gene expressions
#' (printStart), time interval between recordings (printInterval), number of
#' initial conditions (nIC), output precision (outputPrecision), tolerance for
#' adaptive runge kutta method (rkTolerance), parametric variation (paramRange).
#' The list stochParams contains the parameters for stochastic simulations like
#' the number of noise levels to be simulated (nNoise), the ratio of subsequent
#' noise levels (noiseScalingFactor), maximum noise (initialNoise), whether to
#' use same noise for all genes or to scale it as per the median expression of
#' the genes (scaledNoise), ratio of shot noise to additive noise (shotNoise).
#' The list hyperParams contains the parameters like the minimum and maximum
#' production and degration of the genes, fold change, hill coefficient etc.
#' The list options includes logical values like annealing (anneal), scaling of
#' noise (scaledNoise), generation of new initial conditions (genIC), parameters
#' (genParams), whether to integrate or not (integrate), and whether or not to
#' check for limitcycles (limitcycles). The user
#' modifiable simulation options can be specified as other arguments. This
#' list should be used if one wants to modify many settings for multiple
#' simulations.
#' @format list
"configData"

#' @title A circuit with every interaction type for simulations
#' @description This data contains an artificial 4-gene circuit with genes A, B,
#' C, D which contains every possible type of gene interaction simulated by the
#' sRACIPE package. The circuit is designed so that each pair of genes has only
#' one type of interaction and each interaction appears only once, which makes
#' it useful for testing.
#' @format A data frame with 6 rows and 3 variables
"allTypesDemoCircuit"

#' @title A loop motif for demonstrating limit cycles in gene expression
#' @description This data contains the topology for a repressilator circuit of
#' 3 genes cyclically inhibiting each other with transcription factor
#' regulation. This is a simple circuit that can generate limit cycles in gene
#' expression in roughly 5% of models in sRACIPE.
#' @format A data frame with 3 rows and 3 variables.
"repressilator"

#' @title A circuit for modeling the yeast cell cycle
#' @description This data contains a circuit with 15 nodes representing genes
#' involved with the yeast cell cycle.
#' For further details,
#' see Katebi A, Kohar V, Lu M. Random Parametric Perturbations of Gene
#' Regulatory Circuit Uncover State Transitions in Cell Cycle. iScience. 2020
#' Jun 26;23(6):101150. doi: 10.1016/j.isci.2020.101150. Epub 2020 May 11.
#' PMID: 32450514; PMCID: PMC7251928.
#' @format A data frame with 38 rows and 3 variables.
"cellCycle"