GetBonNie for building, analyzing and sharing rule-based models

Bin Hu; G. Matthew Fricke; James R. Faeder; Richard G. Posner; William S. Hlavacek

doi:10.1093/bioinformatics/btp173

GetBonNie for building, analyzing and sharing rule-based models

Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G. Posner, William S. Hlavacek

Biological Sciences

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

Abstract

Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.

Original language	English (US)
Pages (from-to)	1457-1460
Number of pages	4
Journal	Bioinformatics
Volume	25
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btp173
State	Published - Jun 2009

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btp173

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title = "GetBonNie for building, analyzing and sharing rule-based models",

abstract = "Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.",

author = "Bin Hu and {Matthew Fricke}, G. and Faeder, {James R.} and Posner, {Richard G.} and Hlavacek, {William S.}",

note = "Funding Information: Funding: National Institutes of Health (grants GM076570 and CA109552); Department of Energy (contract DE-AC52-06NA25396); and Arizona Biomedical Research Commission.",

year = "2009",

month = jun,

doi = "10.1093/bioinformatics/btp173",

language = "English (US)",

volume = "25",

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T1 - GetBonNie for building, analyzing and sharing rule-based models

AU - Hu, Bin

AU - Matthew Fricke, G.

AU - Faeder, James R.

AU - Posner, Richard G.

AU - Hlavacek, William S.

N1 - Funding Information: Funding: National Institutes of Health (grants GM076570 and CA109552); Department of Energy (contract DE-AC52-06NA25396); and Arizona Biomedical Research Commission.

PY - 2009/6

Y1 - 2009/6

N2 - Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.

AB - Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.

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GetBonNie for building, analyzing and sharing rule-based models

Abstract

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