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是一种计算工具，用于分析单个离子通道的数据。它是一个通用程序，能够处理刺激和数据记录，数据模拟以及解决马尔可夫的倒数问题，即提取产生数据的动力学模型。在过去的15年中，NIH以及NSF，Keck Foundation和IBM资助了它。它每年（免费）每年下载数千次，并在许多出版物中引用。我们亲自培训了150多名来自学术界，行业和政府在年度课程中使用该计划的学生。近年来，该程序已应用于小鼠分子电机，旋转型和睡眠周期的数据分析。它适用于马尔可夫动力学（即状态模型）的任何系统。 Qub是唯一可以在不编程的情况下使用商业或免费的研究人员可用的程序。在过去的二十年中，Qub一直在增长，现在包含大约300,000行代码的四种语言。从未记录过以解决直接问题的许多自定义例程，这些例程已导致一些深奥的代码，这些代码不容易运输。该应用程序建议使用Python重写和文档QUB源代码来处理接口和C ++计算引擎。我们将制作新的代码开源，以便用户可以进行修改。为了减少学习曲线的斜率，菜单将更加层次结构，以便最常见的功能可以使用最少的鼠标/键盘笔触执行。我们将设置Qub来利用在典型的实验室环境中发现的松散耦合的网络计算机，以加快大型数据集和多个模型的处理。我们将创建向导通过仿真和分析来领导外行用户，并在各种主题上创建教学DVD。这些视频将可从我们的Wiki网站下载。公共卫生相关性：该应用程序将为研究控制各种生理功能和疾病的其他分子提供高级工具。