SBMLR

Systems Biology Markup Language (SBML) is widely used by engineers and biochemists as a standard format for representing biochemical systems. The computational environment R is a cutting-edge, open-source tool used broadly by statisticians. R is also the base language and module framework of Bioconductor, a collection of R packages frequently used in DNA microarray data analyses. SBMLR interfaces SBML to R. It is written as an R package which includes an SBML-like R model object of class SBML and several functions which help script writing R users share, edit, test, view and analyze their models. Its structure is shown to the right: 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 odesolve package to simulate SBML models; summary summarizes models, including species and reaction dataframes which contain initial concentrations, initial fluxes, and reaction rate laws (as strings); and == tests the equality of models with respect to these two dataframes.