TRuML: a translator for rule-based modeling languages

Suderman, Ryan T.; Hlavacek, William Scott

doi:10.1145/3107411.3107471

Title: TRuML: a translator for rule-based modeling languages

Conference · Mon Sep 11 00:00:00 EDT 2017

DOI:https://doi.org/10.1145/3107411.3107471· OSTI ID:1392820

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Los Alamos National Laboratory

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC52-06NA25396

OSTI ID:: 1392820

Report Number(s):: LA-UR-17-28151

Resource Relation:: Conference: ACM-BCB ; 2017-08-21 - 2017-08-23 ; Cambridge, Massachusetts, United States

Country of Publication:: United States

Language:: English

References (8)

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems: Computational approach for studying biomolecular site dynamics in cell signaling systems Chylek, Lily A.; Harris, Leonard A.; Tung, Chang-Shung Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 6, Issue 1 https://doi.org/10.1002/wsbm.1245	journal	September 2013
Formal molecular biology Danos, Vincent; Laneve, Cosimo Theoretical Computer Science, Vol. 325, Issue 1 https://doi.org/10.1016/j.tcs.2004.03.065	journal	September 2004
Formal Biochemical Space with Semantics in Kappa and BNGL Děd, T.; Šafránek, D.; Troják, M. Electronic Notes in Theoretical Computer Science, Vol. 326 https://doi.org/10.1016/j.entcs.2016.09.017	journal	October 2016
Stochastic Simulation of Chemical Kinetics Gillespie, Daniel T. Annual Review of Physical Chemistry, Vol. 58, Issue 1 https://doi.org/10.1146/annurev.physchem.58.032806.104637	journal	May 2007
Intrinsic information carriers in combinatorial dynamical systems Harmer, Russ; Danos, Vincent; Feret, Jérôme Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 20, Issue 3 https://doi.org/10.1063/1.3491100	journal	September 2010
Programming biological models in Python using PySB Lopez, Carlos F.; Muhlich, Jeremy L.; Bachman, John A. Molecular Systems Biology, Vol. 9, Issue 1 https://doi.org/10.1038/msb.2013.1	journal	January 2013
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim Sneddon, Michael W.; Faeder, James R.; Emonet, Thierry Nature Methods, Vol. 8, Issue 2 https://doi.org/10.1038/nmeth.1546	journal	December 2010
Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes Suderman, Ryan; Deeds, Eric J. PLoS Computational Biology, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pcbi.1003278	journal	October 2013

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