JSim, an open-source modeling system for data analysis.
JSim, an open-source modeling system for data analysis.
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DOI：
10.12688/f1000research.2-288.v1
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发表时间：
2013-01-01
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影响因子：
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通讯作者：
Bassingthwaighte, James B
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文献类型：
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作者：
Butterworth, Erik;Jardine, Bartholomew E;Bassingthwaighte, James B
JSim是一个模拟系统，用于开发模型，设计实验，并通过对数据的模型解决方案进行测试来评估生理和药理系统的假设。它被设计用于模型代码的交互式、迭代操作，处理多个数据集和参数集，以及在同时运行或单独运行的不同模型之间进行比较。交互式使用由大量图形用户界面支持，用于模型编写和编译诊断、定义输入函数、模型运行、选择求解常微分方程和偏微分方程的算法、运行时多维图形、参数优化（8种方法）、灵敏度分析和用于定义置信范围的蒙特卡罗模拟。JSim使用数学建模语言（MML），一种指定代数和微分方程的声明性语法。用其他语言（MATLAB、FORTRAN、c++等）编写的命令式结构可以通过过程调用来访问。MML语法很简单，基本上是定义参数和变量，然后用简单易懂的数学形式写出方程。这使得JSim既适合教学建模，也适合研究模型分析。对于高吞吐量应用程序，JSim可以作为批处理作业运行。JSim可以自动翻译系统生物学标记语言（SBML）和CellML模型的存储库中的模型。支持随机建模。MML支持将物理单位分配给常量和变量，并自动检查维度平衡，作为验证测试的第一步。自动单位缩放，如秒到分钟，如果需要。JSim项目文件为可重复建模分析设置了一个标准：它在一个文件中包含了分析一组实验的所有内容：数据、模型、数据拟合和参数置信范围的评估。JSim是开源的；它和大约400个人类可读的开源生理/生物物理模型可在http://www.physiome.org/jsim/上获得。
JSim is a simulation system for developing models, designing experiments, and evaluating hypotheses on physiological and pharmacological systems through the testing of model solutions against data. It is designed for interactive, iterative manipulation of the model code, handling of multiple data sets and parameter sets, and for making comparisons among different models running simultaneously or separately. Interactive use is supported by a large collection of graphical user interfaces for model writing and compilation diagnostics, defining input functions, model runs, selection of algorithms solving ordinary and partial differential equations, run-time multidimensional graphics, parameter optimization (8 methods), sensitivity analysis, and Monte Carlo simulation for defining confidence ranges. JSim uses Mathematical Modeling Language (MML) a declarative syntax specifying algebraic and differential equations. Imperative constructs written in other languages (MATLAB, FORTRAN, C++, etc.) are accessed through procedure calls. MML syntax is simple, basically defining the parameters and variables, then writing the equations in a straightforward, easily read and understood mathematical form. This makes JSim good for teaching modeling as well as for model analysis for research. For high throughput applications, JSim can be run as a batch job. JSim can automatically translate models from the repositories for Systems Biology Markup Language (SBML) and CellML models. Stochastic modeling is supported. MML supports assigning physical units to constants and variables and automates checking dimensional balance as the first step in verification testing. Automatic unit scaling follows, e.g. seconds to minutes, if needed. The JSim Project File sets a standard for reproducible modeling analysis: it includes in one file everything for analyzing a set of experiments: the data, the models, the data fitting, and evaluation of parameter confidence ranges. JSim is open source; it and about 400 human readable open source physiological/biophysical models are available at http://www.physiome.org/jsim/.