Algorithms for Molecular Kinetics

分子动力学算法

• 批准号: 8055481
• 负责人: FENG QIN
• 金额: $ 47.32万
• 依托单位: STATE UNIVERSITY OF NEW YORK AT BUFFALO
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-06-01 至 2013-03-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8055481
• 关键词: Academia; Adopted; Algorithms; Code; Computer software; Coupled; Custom; Data; Data Analyses; Data Set; Disease; Documentation; Educational process of instructing; Environment; Foundations; Funding; Government; Health; Industry; Ion Channel; Kinetics; Laboratories; Language; Lead; Learning; Modeling; Modification; Molecular; Molecular Motors; Mus; Physiological; Plug-in; Process; Publications; Pythons; Research Personnel; Site; Sleep; Source Code; Speed; Stimulus; Stroke; Students; System; Time; Training; United States National Institutes of Health; Writing; computer network; computerized tools; experience; improved; open source; parallel computing; portability; programs; simulation; tool; wiki

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.

描述（由申请人提供）：QuB 是传统上用于分析来自单离子通道的数据的计算工具。它是一个通用程序，能够处理刺激和数据记录、数据模拟，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 15 年里，它一直得到 NIH、NSF、Keck 基金会和 IBM 的资助。它每年被下载（免费）数千次，并在许多出版物中被引用。我们在年度课程中亲自培训了来自学术界、工业界和政府的 150 多名学生如何使用该程序。近年来，该程序已应用于分析分子马达、自旋电子学和小鼠睡眠周期的数据。它适用于任何具有马尔可夫动力学特征的系统，即状态模型。 QuB 是研究人员可以使用的唯一一个无需编程即可完成此操作的商业或免费程序。 QuB 在过去 20 年中一直在增长，现在包含四种语言的约 300,000 行代码。许多为解决眼前问题而添加的自定义例程从未被记录下来，这导致了一些不易传输的深奥代码。该应用程序建议使用 Python 来处理接口并使用 C++ 来重写和记录 QuB 源代码作为计算引擎。我们会将新代码开源，以便用户进行修改。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/键盘敲击来执行最常见的功能。我们将设置 QuB，利用典型实验室环境中的松耦合网络计算机来加速大型数据集和多个模型的处理。我们将创建向导来引导非专业用户进行模拟和分析，并创建有关各种主题的教学 DVD。这些视频可以从我们的 wiki 网站下载。公共健康相关性：该应用程序将为研究离子通道和控制各种生理功能和疾病的其他分子提供先进的工具。