Algorithms for Molecular Kinetics

分子动力学算法

• 批准号: 7848858
• 负责人: FENG QIN
• 金额: $ 47.37万
• 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/7848858
• 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; 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; public health relevance; 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，数据的模拟，以及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，它一直由NIH以及NSF、凯克基金会和IBM提供资金。它每年被(免费)下载数千次，并被许多出版物引用。我们亲自培训了来自学术界、工业界和政府部门的150多名学生，在每年的课程中使用该项目。近年来，该程序已被应用于分析来自分子马达、自旋电子学和小鼠睡眠周期的数据。它适用于任何以马尔可夫动力学为特征的系统，即状态模型。QUB是研究人员可以使用的唯一程序，无论是商业的还是免费的，可以在不编程的情况下做到这一点。QUB在过去的二十年里一直在增长，现在包含四种语言的大约300,000行代码。许多为解决即时问题而添加的自定义例程从未被记录在案，这导致了一些难以移植的代码。这个应用程序建议重写和记录QUB源代码，使用Python处理接口，使用C++处理计算引擎。我们将使新代码开放源代码，以便用户可以进行修改。为了减少学习曲线的斜率，菜单将更加层次化，这样最常见的功能就可以通过尽可能少的鼠标/键盘敲击来执行。我们将建立QUB，利用典型实验室环境中松散耦合的联网计算机来加快大数据集和多模型的处理速度。我们将创建向导来引导非专业用户进行模拟和分析，并创建各种主题的教学DVD。这些视频将可从我们的维基网站下载。与公共健康相关：该应用程序将为研究离子通道和其他控制各种生理功能和疾病的分子提供先进的工具。