1. Raue, Bioinformatics 31(21), 2015↩︎

  2. Kaschek, dMod, 2016 (https://cran.r-project.org/package=dMod)↩︎

Imports an SBML model

Requires the presence of IQRsbml (http://www.intiquan.com/iqrsbml).

importSBML_IQRmodel(
  input,
  FLAGexportBC = FALSE,
  FLAGcheckComplete = FALSE,
  FLAGuseSBMLnames = FALSE,
  FLAGremoveSBMLinfo = FALSE,
  filename = NULL,
  FLAGchangeINPUT = FALSE
)

Arguments

input

Path to the SBML XML file

FLAGexportBC

Logical. Imports model in biochemical notation

FLAGcheckComplete

Logical. Checks if SBML model is completely defined

FLAGuseSBMLnames

Logical. Use SBML names instead of IDs ... if not unique then make unique

FLAGremoveSBMLinfo

Logical. Remove additional information

filename

If provided, then converted SBML model will be saved as this file. Otherwise it will be attempted to convert it to an IQRmodel (which might fail if not all defined in the SBML model)

FLAGchangeINPUT

Will revert the IN_PUT to INPUT. If you want to import a model for simulation then use TRUE. If for processing and changing of the model use better FALSE. INPUT* is a reserved word in IQR Tools for handling dosing inputs. Upon export and import of SBML INPUT elements are always represented in ODEs, which might not allow to recognize a state as a specie. Exchanging INPUT to IN_PUT avoids this and the SBML layout is nice. Prior to simulation of doses IN_PUT elements need to be exchanged to INPUT. This is what setting this flag to TRUE does!

Value

IQRmodel imported from SBML