Anatoly Sorokin | Searcharxiv

arXiv2018

RKappa: Software for Analyzing Rule-Based Models

RKappa is a framework for the development, simulation and analysis of rule-base models within the mature statistically empowered R environment. It is designed for model editing, parameter identification, simulation, sensitivity analysis and visualisation. The framework is optimised for high-performance computing platforms and facilitates analysis of large-scale systems biology models where knowledge of exact mechanisms is limited and parameter values are uncertain. The RKappa software is an open source (GLP3 license) package for R, which is freely available online ( https://github.com/lptolik/R4Kappa ).

q-bio.QM↗

arXiv2014

RKappa: Statistical sampling suite for Kappa models

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

q-bio.MN↗