Algorithms for Molecular Kinetics

分子动力学算法

• 批准号: 8247837
• 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 2014-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8247837
• 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; abstracting; computer network; computerized tools; experience; improved; open source; parallel computing; portability; programs; simulation; tool; wiki

Abstract 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 compute 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.

抽象的 QuB 是一种传统上用于分析单离子数据的计算工具 渠道。它是一个能够处理刺激和数据记录的通用程序， 模拟数据，求解提取动力学的逆马尔可夫问题 产生数据的模型。过去 15 年一直由 NIH 和 也由 NSF、Keck 基金会和 IBM 提供。它被下载（免费）数千次 每年多次，并被许多出版物引用。我们亲自培训了150多名 来自学术界、工业界和政府的学生每年都会使用该计划 课程。近年来，该程序已应用于数据分析 分子马达、自旋电子学和小鼠的睡眠周期。适用于任何系统 以马尔可夫动力学为特征，即状态模型。 QuB 是唯一可用于 研究人员，无论是商业的还是免费的，都可以在无需编程的情况下完成此操作。 QuB 在过去 20 年里一直在增长，现在包含大约 300,000 行 四种语言的代码。添加了许多自定义例程来解决 直接的问题从未被记录下来，这些导致了一些深奥的代码 不容易运输。该应用程序建议重写并记录 QuB 使用 Python 处理接口和 C++ 计算引擎的源代码。我们将 将新代码开源，以便用户可以进行修改。为了减少 学习曲线的斜率，菜单将更加分层，以便最常见的 可以用尽可能少的鼠标/键盘操作来执行功能。我们将设置 QuB 可以利用典型的松散耦合的网络计算机 实验室环境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 各种主题的教学 DVD。这些视频可以从以下位置下载 我们的维基网站。