SBMLR

SBMLR provides an R interface for importing, manipulating, analyzing, and exporting Systems Biology Markup Language (SBML) models to support systems biology modeling, parameter estimation, sensitivity analysis, and integration with high-throughput genomic data.

Key Features:

• SBML Compatibility: Supports import and export of SBML files to enable use of SBML-encoded biochemical reaction network models within R.
• Integration with Bioconductor: Enables interoperability with Bioconductor packages for advanced bioinformatic and statistical analyses on imported SBML models.
• Interdisciplinary Research Support: Bridges SBML and R to facilitate combining systems biology models with statistical analysis and high-throughput genomic data.
• R Programming Environment: Leverages R for parameter estimation, sensitivity analysis, model simulation, and manipulation of model components.

Scientific Applications:

• Modeling and Simulation: Simulate SBML models within R to study dynamic behaviors of biological and biochemical networks.
• Parameter Estimation and Optimization: Fit and optimize model parameters to experimental data to improve predictive accuracy.
• Sensitivity Analysis: Perform sensitivity analyses to identify parameters that critically influence system behavior.
• Data Integration: Integrate SBML models with high-throughput genomic data to explore complex networks and pathways.

Methodology:

Import SBML files into R using sbmlr functions; manipulate model components such as species, reactions, and parameters directly within R; utilize Bioconductor packages to perform advanced analyses on imported models; and export modified or analyzed models back to SBML format.