RKappa: Software for Analyzing Rule-Based Models
Anatoly Sorokin, Oksana Sorokina, J. Douglas Armstrong
TL;DR
RKappa is an open-source R package that enables development, simulation, and analysis of rule-based systems biology models, optimized for high-performance computing and large-scale systems with uncertain parameters.
Contribution
It introduces a comprehensive framework within R for rule-based model analysis, combining editing, simulation, and sensitivity analysis capabilities.
Findings
Supports large-scale systems biology models
Facilitates parameter uncertainty analysis
Optimized for high-performance computing
Abstract
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 ).
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Taxonomy
TopicsGene Regulatory Network Analysis · Gene expression and cancer classification · Bioinformatics and Genomic Networks