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BMCBI
2004

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

11 years 1 months ago
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...
Tomas Radivoyevitch
Added 16 Dec 2010
Updated 16 Dec 2010
Type Journal
Year 2004
Where BMCBI
Authors Tomas Radivoyevitch
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