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TRuML: A Translator for Rule-Based Modeling Languages

Authors:

William S. HlavacekAuthors Info & Claims

ACM-BCB '17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics

Pages 372 - 377

https://doi.org/10.1145/3107411.3107471

Published: 20 August 2017 Publication History

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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.

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Cited By

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Wysocka EPage MSnowden JSimpson T(2022)Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling networkPeerJ10.7717/peerj.1451610(e14516)Online publication date: 15-Dec-2022
https://doi.org/10.7717/peerj.14516
Mitra ESuderman RColvin JIonkov AHu ASauro HPosner RHlavacek W(2019)PyBioNetFit and the Biological Property Specification LanguageiScience10.1016/j.isci.2019.08.04519(1012-1036)Online publication date: Sep-2019
https://doi.org/10.1016/j.isci.2019.08.045
Suderman RDeeds E(2018)Intrinsic limits of information transmission in biochemical signalling motifsInterface Focus10.1098/rsfs.2018.00398:6(20180039)Online publication date: 19-Oct-2018
https://doi.org/10.1098/rsfs.2018.0039
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Index Terms

TRuML: A Translator for Rule-Based Modeling Languages
1. Applied computing
  1. Life and medical sciences
    1. Systems biology
2. Computing methodologies
  1. Modeling and simulation
    1. Simulation support systems
      1. Simulation languages

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Information

Published In

ACM-BCB '17: Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics

August 2017

800 pages

ISBN:9781450347228

DOI:10.1145/3107411

General Chairs:
Nurit Haspel
University of Massachusetts Boston, USA
,
Lenore J. Cowen
Tufts University, USA
,
Program Chairs:
Amarda Shehu
George Mason University, USA
,
Tamer Kahveci
University of Florida, USA
,
Giuseppe Pozzi
Politecnico di Milano, Italy

© 2017 Association for Computing Machinery. ACM acknowledges that this contribution was authored or co-authored by an employee, contractor or affiliate of the United States government. As such, the United States Government retains a nonexclusive, royalty-free right to publish or reproduce this article, or to allow others to do so, for Government purposes only.

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 20 August 2017

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Funding Sources

Center for Nonlinear Studies at Los Alamos National Laboratory
National Institutes of Health

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BCB '17

Sponsor:

SIGBio

BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

August 20 - 23, 2017

Massachusetts, Boston, USA

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ACM-BCB '17 Paper Acceptance Rate 42 of 132 submissions, 32%;

Overall Acceptance Rate 254 of 885 submissions, 29%

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Cited By

View all

Wysocka EPage MSnowden JSimpson T(2022)Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling networkPeerJ10.7717/peerj.1451610(e14516)Online publication date: 15-Dec-2022
https://doi.org/10.7717/peerj.14516
Mitra ESuderman RColvin JIonkov AHu ASauro HPosner RHlavacek W(2019)PyBioNetFit and the Biological Property Specification LanguageiScience10.1016/j.isci.2019.08.04519(1012-1036)Online publication date: Sep-2019
https://doi.org/10.1016/j.isci.2019.08.045
Suderman RDeeds E(2018)Intrinsic limits of information transmission in biochemical signalling motifsInterface Focus10.1098/rsfs.2018.00398:6(20180039)Online publication date: 19-Oct-2018
https://doi.org/10.1098/rsfs.2018.0039
Suderman RMitra ELin YErickson KFeng SHlavacek W(2018)Generalizing Gillespie’s Direct Method to Enable Network-Free SimulationsBulletin of Mathematical Biology10.1007/s11538-018-0418-2Online publication date: 28-Mar-2018
https://doi.org/10.1007/s11538-018-0418-2
Mitra ESuderman RColvin JIonkov AHu ASauro HPosner RHlavacek W(undefined)PyBioNetFit and the Biological Property Specification LanguageSSRN Electronic Journal10.2139/ssrn.3382545
https://doi.org/10.2139/ssrn.3382545

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