RKappa: Statistical sampling suite for Kappa models

TL;DR

RKappa is a comprehensive R-based framework for developing, analyzing, and visualizing rule-based models with statistical sampling, enabling efficient sensitivity analysis and large-scale system exploration in biological research.

Contribution

It introduces RKappa, a novel R package that integrates model editing, parameter sampling, simulation, and analysis for rule-based models within a high-performance computing framework.

Findings

Effective global sensitivity analysis demonstrated

Supports parallel and concurrent computations

Applicable to large-scale biological systems

Abstract

We present RKappa, a framework for the development and analysis of rule-based models within a mature, statistically empowered R environment. The infrastructure allows model editing, modification, parameter sampling, simulation, statistical analysis and visualisation without leaving the R environment. We demonstrate its effectiveness through its application to Global Sensitivity Analysis, exploring it in "parallel" and "concurrent" implementations. The pipeline was designed for high performance computing platforms and aims to facilitate analysis of the behaviour of large-scale systems with limited knowledge of exact mechanisms and respectively sparse availability of parameter values, and is illustrated here with two biological examples. The package is available on github: https://github.com/lptolik/R4Kappa