BioNetFit: A fitting tool compatible with BioNetGen, NFsim and distributed computing environments

Brandon R. Thomas; Lily A. Chylek; Joshua Colvin; Suman Sirimulla; Andrew H.A. Clayton; William S. Hlavacek; Richard G. Posner

doi:10.1093/bioinformatics/btv655

BioNetFit: A fitting tool compatible with BioNetGen, NFsim and distributed computing environments

Brandon R. Thomas, Lily A. Chylek, Joshua Colvin, Suman Sirimulla, Andrew H.A. Clayton, William S. Hlavacek, Richard G. Posner

Biological Sciences

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

26 Scopus citations

Abstract

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.

Original language	English (US)
Pages (from-to)	798-800
Number of pages	3
Journal	Bioinformatics
Volume	32
Issue number	5
DOIs	https://doi.org/10.1093/bioinformatics/btv655
State	Published - Mar 1 2016

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/btv655

Cite this

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abstract = "Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.",

author = "Thomas, {Brandon R.} and Chylek, {Lily A.} and Joshua Colvin and Suman Sirimulla and Clayton, {Andrew H.A.} and Hlavacek, {William S.} and Posner, {Richard G.}",

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doi = "10.1093/bioinformatics/btv655",

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AU - Thomas, Brandon R.

AU - Chylek, Lily A.

AU - Colvin, Joshua

AU - Sirimulla, Suman

AU - Clayton, Andrew H.A.

AU - Hlavacek, William S.

AU - Posner, Richard G.

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AB - Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.

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BioNetFit: A fitting tool compatible with BioNetGen, NFsim and distributed computing environments

Abstract

ASJC Scopus subject areas

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