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A two-way interface between limited Systems Biology Markup Language and R
1Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio 44106, USA. radivot@hal.cwru.edu
BMC Bioinformatics
|December 9, 2004
Summary
A new interface now allows Systems Biology Markup Language (SBML) models to be read and written in R, a popular statistical environment. This facilitates data exchange for dynamical systems analysis in R and SBML users.
Area of Science:
- Computational Biology
- Systems Biology
- Bioinformatics
Background:
- Systems Biology Markup Language (SBML) is a standard for dynamical systems data representation.
- R is a widely used open-source environment for statistical analysis, particularly in biostatistics and microarray analysis.
- Currently, no interface exists between SBML and R, limiting interoperability.
Purpose of the Study:
- To develop an interface enabling data exchange between SBML and R.
- To facilitate the use of SBML models within the R environment for dynamical systems analysis.
- To bridge the gap for users interested in both SBML and R.
Main Methods:
- An R model structure was defined, partially mirroring SBML.
- Two functions, write.SBML() and read.SBML(), were developed for bidirectional mapping.
- write.SBML() maps the R structure to SBML Level 2.
- read.SBML() maps a subset of SBML Level 2 files back into R.
Main Results:
- A functional interface between R and SBML was successfully created.
- A published purine metabolism model was used to test the interface.
- The mapped model accurately reproduced published time-course responses, validating the interface's performance.
Conclusions:
- R's inherent list infrastructure is suitable for manipulating SBML models.
- The developed SBML-R interface enhances the utility of both systems.
- Further development of this interface is recommended to expand its capabilities.