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

Abstract

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here in this paper, 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.

Authors:
 [1];  [2];  [1];  [3];  [4];  [5];  [1]
  1. Northern Arizona Univ., Flagstaff, AZ (United States). Dept. of Biological Sciences
  2. Cornell Univ., Ithaca, NY (United States). Baker Lab., Dept. of Chemistry and Chemical Biology; Northern Arizona Univ., Flagstaff, AZ (United States). Dept. of Biological Sciences
  3. Saint Louis College of Pharmacy, Saint Louis, MO (United States). Dept. of Basic Sciences
  4. Swinburne Univ. of Technology, Hawthorn, VIC (Australia). Center for Microphotonics, Faculty of Science, Engineering and Technology, Cell Biophysics Lab.
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
Work for Others (WFO); National Institutes of Heath (NIH); USDOE
OSTI Identifier:
1406198
Report Number(s):
LA-UR-15-25157
Journal ID: ISSN 1367-4803
Grant/Contract Number:  
AC52-06NA25396; R01GM111510
Resource Type:
Accepted Manuscript
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Volume: 32; Journal Issue: 5; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Biological Science

Citation Formats

Thomas, Brandon R., Chylek, Lily A., Colvin, Joshua, Sirimulla, Suman, Clayton, Andrew H. A., Hlavacek, William S., and Posner, Richard G. BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. United States: N. p., 2015. Web. doi:10.1093/bioinformatics/btv655.
Thomas, Brandon R., Chylek, Lily A., Colvin, Joshua, Sirimulla, Suman, Clayton, Andrew H. A., Hlavacek, William S., & Posner, Richard G. BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. United States. doi:10.1093/bioinformatics/btv655.
Thomas, Brandon R., Chylek, Lily A., Colvin, Joshua, Sirimulla, Suman, Clayton, Andrew H. A., Hlavacek, William S., and Posner, Richard G. Mon . "BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments". United States. doi:10.1093/bioinformatics/btv655. https://www.osti.gov/servlets/purl/1406198.
@article{osti_1406198,
title = {BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments},
author = {Thomas, Brandon R. and Chylek, Lily A. and Colvin, Joshua and Sirimulla, Suman and Clayton, Andrew H. A. and Hlavacek, William S. and Posner, Richard G.},
abstractNote = {Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here in this paper, 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.},
doi = {10.1093/bioinformatics/btv655},
journal = {Bioinformatics},
number = 5,
volume = 32,
place = {United States},
year = {2015},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 6 works
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