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

Journal Article · · Bioinformatics
 [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)
+ Show Author Affiliations

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.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
National Institutes of Heath (NIH); USDOE; Work for Others (WFO)
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1406198
Report Number(s):
LA-UR-15-25157
Journal Information:
Bioinformatics, Journal Name: Bioinformatics Journal Issue: 5 Vol. 32; ISSN 1367-4803
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

References (9)

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  • 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
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Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates journal January 2010
Recruitment of the Adaptor Protein Grb2 to EGFR Tetramers journal April 2014
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim journal December 2010
Exploring higher-order EGFR oligomerisation and phosphorylation—a combined experimental and theoretical approach journal January 2013
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Cited By (13)

PyBioNetFit and the Biological Property Specification Language journal September 2019
Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation journal November 2017
Pleione: A tool for statistical and multi-objective calibration of Rule-based models journal October 2019
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor journal January 2019
Using both qualitative and quantitative data in parameter identification for systems biology models journal September 2018
Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks journal June 2019
BioNetGen 2.2: advances in rule-based modeling journal July 2016
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model journal July 2019
Intrinsic limits of information transmission in biochemical signalling motifs journal October 2018
Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor journal January 2019
From word models to executable models of signaling networks using automated assembly journal November 2017
Allergen Valency, Dose, and FcεRI Occupancy Set Thresholds for Secretory Responses to Pen a 1 and Motivate Design of Hypoallergens journal December 2016
Scaling methods for accelerating kinetic Monte Carlo simulations of chemical reaction networks text January 2019

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
Biological Science