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 ma...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Tomas Radivoyevitch
• Keywords: BMCBI 2004, SBML, SBML Level, Systems Biology Markup Language