A two-way interface between limited Systems Biology Markup Language and R.
BACKGROUND
Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures. The open source statistical programming environment R is widely used by biostatisticians involved in microarray analyses. An interface between SBML and R does not exist, though one might be useful to R users interested in SBML, and SBML users interested in R.


RESULTS
A model structure that parallels SBML to a limited degree is defined in R. An interface between this structure and SBML is provided through two function definitions: write.SBML() which maps this R model structure to SBML level 2, and read.SBML() which maps a limited range of SBML level 2 files back to R. A published model of purine metabolism is provided in this SBML-like format and used to test the interface. The model reproduces published time course responses before and after its mapping through SBML.


CONCLUSIONS
List infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted.
Radivoyevitch
Tomas
T
Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA. radivot@hal.cwru.edu
D007802:Language; D012984:Software; D049490:Systems Biology / Q000145:classification* / Q000379:methods*