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

Tomas Radivoyevitch

doi:10.1186/1471-2105-5-190

Tomas Radivoyevitch

Open Access

https://doi.org/10.1186/1471-2105-5-190

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Journal: BMC bioinformatics	Publication Date: Jan 1, 2004
Citations: 10	License type: CC BY 2.0

Affiliation: Case Western Reserve University

Abstract

BackgroundSystems 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.ResultsA 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.ConclusionsList infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted.

Highlights

Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures
This paper provides an explicit example of one approach to an SBML-R interface
The SBML file could be imported into visualization packages such as JDesigner [13]

Summary

Introduction

Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures. Systems biology markup language (SBML) is a standard for representing dynamical systems of biological interest [1,2]. Interfaces between SBML and high level computational environments are currently being developed for Mathematica [3] and Matlab [4], but to the author's knowledge, no such efforts are being carried forth for R/Splus. This brief paper presents the author's initial developments toward a two-way SBML-R interface. The interface is currently limited in the range of SBML input files that it can handle. It is assumed throughout that the reader is already quite familiar with both SBML [8] and R [9]

Results

Discussion

Conclusion