A Step-by-Step Guide to Using BioNetFit.
A Step-by-Step Guide to Using BioNetFit.
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使用 BioNetFit 的分步指南。
DOI：
10.1007/978-1-4939-9102-0_18
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Posner,RichardG
中科院分区：
文献类型：
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作者：
Hlavacek,WilliamS;Csicsery-Ronay,JenniferA;Baker,LewisR;RamosÁlamo,MaríaDelCarmen;Ionkov,Alexander;Mitra,EshanD;Suderman,Ryan;Erickson,KeeshaE;Dias,Raquel;Colvin,Joshua;Thomas,BrandonR;Posner,RichardG
BioNetFit是一个软件工具，用于解决在基于规则的模型开发中出现的参数识别问题。它通过曲线拟合（即，非线性回归）。BioNetFit与接受BioNetGen语言（BNGL）格式的文件作为输入的确定性和随机模拟器兼容，例如BioNetGen框架内提供的文件。BioNetFit可以在笔记本电脑或独立的多核工作站上使用，也可以在许多Linux集群上使用，比如那些使用Slurm集群管理器来调度作业的集群。BioNetFit实现了一种基于种群的元启发式全局优化程序，一种进化算法（EA），以最小化用户定义的目标函数，例如残差平方和（RSS）函数。BioNetFit还实现了一个自举程序，用于确定参数估计的置信区间。在这里，我们提供了使用BioNetFit来估计BNGL编码模型的参数值和定义Bootstrap置信区间的分步说明。该过程需要使用几个纯文本文件，这些文件由BioNetFit和BioNetGen处理。通常，这些文件包括（1）一个或多个EXP文件，每个EXP文件包含（2）包含模型部分的BNGL文件，该模型部分定义了（基于规则的）模型，以及动作部分，其定义生成GDAT和/或SCAN文件的仿真协议，所述GDAT和/或SCAN文件具有对应于EXP文件中的数据的模型预测;以及（3）配置拟合/自举作业并定义算法参数设置的CONF文件。
BioNetFit is a software tool designed for solving parameter identification problems that arise in the development of rule-based models. It solves these problems through curve fitting (i.e., nonlinear regression). BioNetFit is compatible with deterministic and stochastic simulators that accept BioNetGen language (BNGL)-formatted files as inputs, such as those available within the BioNetGen framework. BioNetFit can be used on a laptop or stand-alone multicore workstation as well as on many Linux clusters, such as those that use the Slurm Workload Manager to schedule jobs. BioNetFit implements a metaheuristic population-based global optimization procedure, an evolutionary algorithm (EA), to minimize a user-defined objective function, such as a residual sum of squares (RSS) function. BioNetFit also implements a bootstrapping procedure for determining confidence intervals for parameter estimates. Here, we provide step-by-step instructions for using BioNetFit to estimate the values of parameters of a BNGL-encoded model and to define bootstrap confidence intervals. The process entails the use of several plain-text files, which are processed by BioNetFit and BioNetGen. In general, these files include (1) one or more EXP files, which each contains (experimental) data to be used in parameter identification/bootstrapping; (2) a BNGL file containing a model section, which defines a (rule-based) model, and an actions section, which defines simulation protocols that generate GDAT and/or SCAN files with model predictions corresponding to the data in the EXP file(s); and (3) a CONF file that configures the fitting/bootstrapping job and that defines algorithmic parameter settings.