Paper Info
Title
Multi-level modeling and simulation of cell biological systems with ML-Rules - A tutorial
Abstract
Multi-level modeling is concerned with describing a system at different levels of organization and relating their dynamics. ML-Rules is a rule-based language developed for supporting the modeling of cell biological systems. It supports nested rule schemata, the hierarchical dynamic nesting of species, the assignment of attributes and solutions to species at each level, and a flexible definition of reaction rate kinetics. As ML-Rules allows the compact description of rather complex models, means for an efficient execution were developed, e.g., approximate and adaptive algorithms. Experimentation with ML-Rules models is further supported by domain-specific languages for instrumentation and experimentation which have been developed in the context of the modeling and simulation framework JAMES II. A signaling pathway example will illustrate modeling and simulation with ML-Rules.
Year
DOI
Venue
2014
10.1109/WSC.2014.7019887
WSC '14: Winter Simulation Conference Savannah Georgia December, 2014
Keywords
Field
DocType
bioinformatics,cellular biophysics,logic programming,reaction kinetics,JAMES-II modeling-and-simulation framework,ML-Rules,adaptive algorithms,approximate algorithms,attribute assignment,cell biological system modeling,cell biological systems,domain-specific languages,hierarchical dynamic species nesting,multilevel modeling,multilevel simulation,nested rule schemata,reaction rate kinetics,rule-based language,signaling pathway
Computer science,Simulation,Modeling and simulation,Multilevel model,Modeling language,Theoretical computer science,Systems modeling,Schema (psychology)
Conference
ISSN
ISBN
Citations 
0891-7736
978-1-4673-9741-4
2
PageRank 
References 
Authors
0.37
36
4
Name
Order
Citations
PageRank
Tobias Helms120.37
Carsten Maus220.37
Fiete Haack321.04
Adelinde M. Uhrmacher41089.41