The sbmlpbk package

An R package for importing Physiologically Based Kinetic (PBK) models encoded in the Systems Biology Markup Language (SBML) format, enabling simulation using the deSolve package. This package is still under development.

Installation

Install from GitHub (using the remotes package):

remotes::install_github("Biometris/sbmlpbk", ref = "main", dependencies = TRUE)

Quickstart

To load an SBML model from a file, simply use the load_sbml function. The following example loads the file simple_oral.sbml provided with the package:

# Load package
library(sbmlpbk)

# Get filename
file_simple_oral <- system.file("extdata/", "simple_oral.sbml", package = "sbmlpbk")

# Load model
model <- load_sbml(file_simple_oral)

# Get model summary
summary(model)

The code below shows how to run simulations using the ode function of deSolve.

# Load package deSolve
library(deSolve)

# Load model functions
load_functions(model)

# Load params
params_csv <- system.file("extdata/", "simple_oral_params.csv", package = "sbmlpbk")
params <- load_params(model, file = params_csv, param_instance = "simple_PARAM")

# Set input species
input_species <- "AGut"

# Set input events (single unit bolus at time 1)
eventdat <- data.frame(var = c(input_species), time = c(1), value = c(1), method = c("add"))

# Set initial states
initial_states <- setNames(rep(0, length(model$species)), names(model$species))

# Set simulation times
times <- seq(0, 40, 1)

# Load deSolve model function
func <- create_desolve_func(model)

# Simulate
out <- ode(
  y = initial_states,
  times = times,
  func = func,
  parms = params,
  events = list(data = eventdat)
)

# Plot results
plot(out)

Detailed example

For a more details, see the vignette.

vignette('sbmlpbk', package='sbmlpbk')