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

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

作者机构：No Arizona Univ Dept Biol Sci Box 5640 Flagstaff AZ 86011 USA Cornell Univ Dept Chem & Chem Biol Ithaca NY USA St Louis Coll Pharm Dept Basic Sci St Louis MO USA Swinburne Univ Technol Fac Sci Engn & Technol Cell Biophys Lab Ctr Microphoton Hawthorn Vic 3122 Australia Los Alamos Natl Lab Div Theoret Los Alamos NM USA 

出 版 物：《BIOINFORMATICS》 (生物信息学)

年 卷 期：2016年第32卷第5期

页      面：798-800页

核心收录：

学科分类：0710[理学-生物学] 08[工学] 0714[理学-统计学（可授理学、经济学学位）] 0836[工学-生物工程] 0812[工学-计算机科学与技术（可授工学、理学学位）] 

基　　金：NIH/NIGMS [R01GM111510] Arizona's Technology and Research Initiative Fund 

主　　题：Distributed computing Computer networks Distributed sensors Cyberinfrastructure Computer systems 

摘      要：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.