Algorithms for Molecular Kinetics

描述（由申请人提供）：QuB是一种传统上用于分析单离子通道数据的计算工具。它是一个通用程序，能够处理刺激和数据记录，模拟数据，并解决提取产生数据的动力学模型的逆马尔可夫问题。在过去的15年里，它得到了NIH、NSF、凯克基金会和IBM的资助。它每年被下载（免费）数千次，并被许多出版物引用。我们已经在年度课程中亲自培训了来自学术界，工业界和政府的150多名学生使用该计划。近年来，该程序已被应用于分子马达、自旋电子学和小鼠睡眠周期的数据分析。它适用于任何以马尔可夫动力学为特征的系统，即状态模型。QuB是唯一一个可供研究人员使用的程序，无论是商业的还是免费的，都可以在没有编程的情况下做到这一点。QuB在过去的20年里一直在增长，现在包含大约30万行四种语言的代码。为解决眼前问题而添加的许多自定义例程从未记录下来，这导致了一些难以传输的深奥代码。该应用程序建议使用Python重写和记录QuB源代码来处理接口和C++计算引擎。我们将使新代码开源，以便用户可以进行修改。为了降低学习曲线的斜率，菜单将更加分层，以便可以用尽可能少的鼠标/键盘敲击执行最常见的功能。我们将建立QuB，以利用典型实验室环境中的松散耦合网络计算机来加速处理大型数据集和多个模型。我们将创建向导，引导外行用户通过模拟和分析，并创建各种主题的教学DVD。这些视频可以从我们的wiki网站下载。公共卫生相关性：该应用将为研究控制各种生理功能和疾病的离子通道和其他分子提供先进的工具。

DESCRIPTION (provided by applicant): QuB is a computational tool used traditionally to analyze the data from single ion channels. It is a general program capable of handling stimulus and data recording, the simulation of data, and solving the inverse Markov Problem of extracting the kinetic model that produced the data. It has been funded for the last 15 years by the NIH and also by NSF, the Keck Foundation, and IBM. It is downloaded (for free) thousands of times a year and is cited in many publications. We have personally trained more than 150 students from academia, industry and government in use of the program at an annual course. In recent years the program has been applied to the analysis of data from molecular motors, spintronics and the sleep cycles in mice. It applies to any system characterized by Markov kinetics, i.e. state models. QuB is the only program available to researchers, commercial or free, that can do this without programming. QuB has been growing for the last twenty years and now contains about 300,000 lines of code in four languages. Many of the custom routines that have been added to solve immediate problems were never documented and these have lead to some esoteric code that is not readily transported. This application proposes to rewrite and document QuB source code using Python to handle the interfaces and C++ the computing engines. We will make the new code open source so that users can make modifications. To decrease the slope of the learning curve, the menus will be more hierarchical so that the most common functions can be executed with the fewest possible mouse/keyboard strokes. We will set up QuB to utilize the loosely coupled networked computers found in the typical laboratory environment to speed up the processing of large data sets and multiple models. We will create Wizards to lead the lay user through simulation and analysis and create instructional DVDs on various topics. These videos will be available for download from our wiki site. PUBLIC HEALTH RELEVANCE: The application will provide advanced tools for studying ion channels and other molecules that control various physiological functions and diseases.