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Open Access Software

A two-way interface between limited Systems Biology Markup Language and R

Tomas Radivoyevitch

Author Affiliations

Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106 USA

BMC Bioinformatics 2004, 5:190  doi:10.1186/1471-2105-5-190

Published: 7 December 2004

Abstract

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.