SBMLR

SBMLR

Systems Biology Markup Language (SBML) is a standard format for representing biochemical systems. The computational environment R is an open-source tool used broadly by statisticians. SBMLR interfaces SBML to R. It is written as an R package that includes an SBML-like R model object of class SBML and several functions that help script writing R users share, edit, test, view and analyze their models. Its structure is shown below: saveSBML exports SBML model objects to SBML level 2 model files; readSBML imports a limited range of SBML level 2 model files back to SBMLR (events, algebraic rules and function definitions have not yet been implemented); saveSBMLR and readSBMLR exchange SBML objects with SBMLR model definition files used for model editing; simulate uses lsoda of R's deSolve package to simulate SBML models; summary summarizes models, including species and reaction dataframes that contain initial concentrations, initial fluxes, and reaction rate laws (as strings); and == tests the equality of models with respect to these two dataframes.