Paper Info
Title
TRuML: A Translator for Rule-Based Modeling Languages
Abstract
Rule-based modeling languages, such as the Kappa and BioNetGen languages (BNGL), are powerful frameworks for modeling the dynamics of complex biochemical reaction networks. Each language is distributed with a distinct software suite and modelers may wish to take advantage of both toolsets. This paper introduces a practical application called TRuML that translates models written in either Kappa or BNGL into the other language. While similar in many respects, key differences between the two languages makes translation sufficiently complex that automation becomes a useful tool. TRuML accommodates the languages' complexities and produces a semantically equivalent model in the alternate language of the input model when possible and an approximate model in certain other cases. Here, we discuss a number of these complexities and provide examples of equivalent models in both Kappa and BNGL.
Year
DOI
Venue
2017
10.1145/3107411.3107471
BCB
Keywords
Field
DocType
Kappa,BNGL,rule-based modeling,systems biology,reaction network modeling,domain-specific languages
Domain-specific language,Rule-based modeling,Second-generation programming language,Computer science,Software suite,Modeling language,Automation,Theoretical computer science,Semantic equivalence
Conference
ISBN
Citations 
PageRank 
978-1-4503-4722-8
0
0.34
References 
Authors
2
2
Name
Order
Citations
PageRank
Ryan Suderman100.68
William S. Hlavacek227724.15