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BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.
Brandon R Thomas1, Lily A Chylek2, Joshua Colvin1
1Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
Bioinformatics (Oxford, England)
|November 12, 2015
Summary
BioNetFit is a new tool that optimizes parameter values for rule-based models, improving consistency with simulation data. It leverages distributed computing for computationally expensive model fitting.
Area of Science:
- Systems Biology
- Computational Biology
- Biophysics
Background:
- Rule-based modeling is crucial for analyzing complex biological systems.
- Specialized simulators like BioNetGen and NFsim are used for rule-based model analysis.
- Parameter fitting is essential for reconciling model predictions with experimental data.
Purpose of the Study:
- To introduce BioNetFit, a versatile fitting tool for rule-based models.
- To enhance the compatibility of fitting procedures with existing simulators (BioNetGen, NFsim).
- To facilitate computationally intensive parameter optimization using distributed computing.
Main Methods:
- BioNetFit is a general-purpose fitting tool compatible with BioNetGen and NFsim.
- The software is designed to utilize distributed computing resources.
- Parameter optimization is achieved through fitting simulations to data.
Main Results:
- BioNetFit enables efficient parameter value optimization for rule-based models.
- The tool supports computationally expensive simulations by employing distributed computing.
- It ensures consistency between model parameters and experimental data.
Conclusions:
- BioNetFit provides a robust solution for parameter fitting in rule-based modeling.
- Its compatibility and distributed computing capabilities make it valuable for systems biology research.
- The tool enhances the predictive power of computational models by improving parameter accuracy.
