BioNetGen 2.2: Advances in Rule-based Modeling

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2016 Jul 13

PMID 27402907

Citations 105

Authors

Leonard A Harris

Justin S Hogg

Jose-Juan Tapia

John A P Sekar

Sanjana Gupta

Ilya Korsunsky

Arshi Arora

Dipak Barua

Robert P Sheehan

James R Faeder

Affiliations

Soon will be listed here.

Abstract

Availability And Implementation: Stable BioNetGen releases (Linux, Mac OS/X and Windows), with documentation, are available at http://bionetgen.org Source code is available at http://github.com/RuleWorld/bionetgen CONTACT: bionetgen.help@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.

Citing Articles

Data Hazards as An Ethical Toolkit for Neuroscience.

Garcia S, Welsh C, Di Cara N, Sterratt D, Romano N, Stefan M Neuroethics. 2025; 18(1):15.

PMID: 39980970 PMC: 11835915. DOI: 10.1007/s12152-024-09580-3.

Leveraging public AI tools to explore systems biology resources in mathematical modeling.

Kannan M, Bridgewater G, Zhang M, Blinov M NPJ Syst Biol Appl. 2025; 11(1):15.

PMID: 39910106 PMC: 11799200. DOI: 10.1038/s41540-025-00496-z.

A detailed kinetic model of Eastern equine encephalitis virus replication in a susceptible host cell.

Larkin C, Dunn M, Shoemaker J, Klimstra W, Faeder J bioRxiv. 2025; .

PMID: 39764060 PMC: 11703215. DOI: 10.1101/2024.12.13.628424.

Expressive rule-based modeling and fast simulation for dynamic compartments.

Koster T, Henning P, Warnke T, Uhrmacher A PLoS One. 2024; 19(10):e0312813.

PMID: 39480777 PMC: 11527154. DOI: 10.1371/journal.pone.0312813.

Algebraic and diagrammatic methods for the rule-based modeling of multi-particle complexes.

Rousseau R, Kinney J ArXiv. 2024; .

PMID: 39279831 PMC: 11398547.

References

Xu W, Smith A, Faeder J, Marai G . RuleBender: a visual interface for rule-based modeling. Bioinformatics. 2011; 27(12):1721-2. PMC: 3106190. DOI: 10.1093/bioinformatics/btr197. View

Hogg J, Harris L, Stover L, Nair N, Faeder J . Exact hybrid particle/population simulation of rule-based models of biochemical systems. PLoS Comput Biol. 2014; 10(4):e1003544. PMC: 3974646. DOI: 10.1371/journal.pcbi.1003544. View

Earl D, Deem M . Parallel tempering: theory, applications, and new perspectives. Phys Chem Chem Phys. 2009; 7(23):3910-6. DOI: 10.1039/b509983h. View

Chylek L, Harris L, Tung C, Faeder J, Lopez C, Hlavacek W . Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdiscip Rev Syst Biol Med. 2013; 6(1):13-36. PMC: 3947470. DOI: 10.1002/wsbm.1245. View

Misirli G, Cavaliere M, Waites W, Pocock M, Madsen C, Gilfellon O . Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. Bioinformatics. 2015; 32(6):908-17. PMC: 4803388. DOI: 10.1093/bioinformatics/btv660. View

Klinke 2nd D . In silico model-based inference: a contemporary approach for hypothesis testing in network biology. Biotechnol Prog. 2014; 30(6):1247-61. PMC: 4261023. DOI: 10.1002/btpr.1982. View

Sneddon M, Faeder J, Emonet T . Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat Methods. 2010; 8(2):177-83. DOI: 10.1038/nmeth.1546. View

Wenskovitch Jr J, Harris L, Tapia J, Faeder J, Marai G . MOSBIE: a tool for comparison and analysis of rule-based biochemical models. BMC Bioinformatics. 2014; 15:316. PMC: 4261755. DOI: 10.1186/1471-2105-15-316. View

Kerr R, Bartol T, Kaminsky B, Dittrich M, Chang J, Baden S . FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES. SIAM J Sci Comput. 2010; 30(6):3126. PMC: 2819163. DOI: 10.1137/070692017. View

10.

Chylek L, Harris L, Faeder J, Hlavacek W . Modeling for (physical) biologists: an introduction to the rule-based approach. Phys Biol. 2015; 12(4):045007. PMC: 4526164. DOI: 10.1088/1478-3975/12/4/045007. View

11.

Hucka M, Finney A, Sauro H, Bolouri H, Doyle J, Kitano H . The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003; 19(4):524-31. DOI: 10.1093/bioinformatics/btg015. View

12.

Marchisio M . Parts & pools: a framework for modular design of synthetic gene circuits. Front Bioeng Biotechnol. 2014; 2:42. PMC: 4186347. DOI: 10.3389/fbioe.2014.00042. View

13.

Eydgahi H, Chen W, Muhlich J, Vitkup D, Tsitsiklis J, Sorger P . Properties of cell death models calibrated and compared using Bayesian approaches. Mol Syst Biol. 2013; 9:644. PMC: 3588908. DOI: 10.1038/msb.2012.69. View

14.

Harris L, Clancy P . A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics. J Chem Phys. 2006; 125(14):144107. DOI: 10.1063/1.2354085. View

15.

Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V . BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol. 2010; 4:92. PMC: 2909940. DOI: 10.1186/1752-0509-4-92. View

16.

Moraru I, Schaff J, Slepchenko B, Blinov M, Morgan F, Lakshminarayana A . Virtual Cell modelling and simulation software environment. IET Syst Biol. 2008; 2(5):352-62. PMC: 2711391. DOI: 10.1049/iet-syb:20080102. View

17.

Gillespie D . Stochastic simulation of chemical kinetics. Annu Rev Phys Chem. 2006; 58:35-55. DOI: 10.1146/annurev.physchem.58.032806.104637. View

18.

Lopez C, Muhlich J, Bachman J, Sorger P . Programming biological models in Python using PySB. Mol Syst Biol. 2013; 9:646. PMC: 3588907. DOI: 10.1038/msb.2013.1. View

19.

Thomas B, Chylek L, Colvin J, Sirimulla S, Clayton A, Hlavacek W . BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. Bioinformatics. 2015; 32(5):798-800. PMC: 4907397. DOI: 10.1093/bioinformatics/btv655. View

20.

Faeder J, Blinov M, Hlavacek W . Rule-based modeling of biochemical systems with BioNetGen. Methods Mol Biol. 2009; 500:113-67. DOI: 10.1007/978-1-59745-525-1_5. View