RT Journal Article SR Electronic T1 TRuML: A Translator for Rule-Based Modeling Languages JF bioRxiv FD Cold Spring Harbor Laboratory SP 171306 DO 10.1101/171306 A1 Ryan Suderman A1 William S. Hlavacek YR 2017 UL http://biorxiv.org/content/early/2017/08/01/171306.abstract AB 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.CCS CONCEPTS • Applied computing → Systems biology; • Computing methodologies → Simulation languages;