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RKappa: Statistical sampling suite for Kappa models

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Original languageEnglish
Title of host publicationHybrid Systems Biology
Subtitle of host publicationSecond International Workshop, HSB 2013, Taormina, Italy, September 2, 2013 and Third International Workshop, HSB 2014, Vienna, Austria, July 23-24, 2014, Revised Selected Papers
PublisherSpringer International Publishing
Number of pages15
ISBN (Electronic)978-3-319-27656-4
ISBN (Print)978-3-319-27655-7
DOIs
Publication statusPublished - 2014

Publication series

NameLecture Notes in Computer Science
PublisherSpringer International Publishing
Volume7699
ISSN (Print)0302-9743

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.

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