ABI Sustaining: Maintaining CHARMM-GUI to Support the Biomolecular Modeling and Simulation Community

ABI 维持：维护 CHARMM-GUI 以支持生物分子建模和模拟社区

基本信息

批准号：
1660380
负责人：
Wonpil Im
金额：
$ 65.93万
依托单位：
Lehigh University
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2017
资助国家：
美国
起止时间：
2017-08-01 至 2022-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1660380&HistoricalAwards=false
关键词：
ABI Sustaining Maintaining CHARMM GUI

项目摘要

Researchers who study how biomolecules flex or shift shape over time use very sophisticated algorithms as tools to understand different aspects of structure, motion and interaction. These tools are part of larger software applications that capture how the whole system behaves, including atoms and molecules that are in both the environment and the biomolecules. As researchers model larger volumes with more components, over longer study intervals, keeping track of all the elements in the system and their properties is becoming a major hurdle, even for relatively well-experienced computational biologists. The grand challenge is to maintain accuracy and reproducibility while efficiently carrying out these complex simulations in order to solve practical problems. The goal of this project is to assist two classes of researchers: experts who know how to set up the conditions and want to save and share them, and non-experts who need guidance in setting up all of the inputs and perhaps some help with interpreting the results. These challenges have been addressed by CHARMM-GUI, in that users can interactively set up complex biomolecular systems and easily understand what files must be input in order to carry out state-of-the-art biomolecular simulations. The interface is not limited to the CHARMM simulation package, despite the name, but also encompasses GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. This project aims to maintain the unique scope of the CHARMM-GUI interface application while improving the consistency of the code base to make it easier to maintain the tool going forward, and to make it easier to add new functionality that works correctly by including test suites. The project's overarching goal is to help students and researchers carry out innovative and novel biomolecular modeling and simulation research to acquire novel insight into structures, dynamics, and underlying mechanisms for the biomolecular systems of interest through availability of an excellent tool, excellent documentation with tutorials, Webinars and videos, and a user forum.The main objective of this project is to ensure ongoing maintenance for the operation of CHARMM-GUI (http://www.charmm-gui.org), a web-based graphical user interface (GUI). This will require code changes to make it a robust, sustainable web-based cyberinfrastructure that supports both expert and non-expert users from a broad range of disciplines to easily build and simulate complex biological systems. Over the past 10 years, CHARMM-GUI has proven that such a web-based GUI provides an ideal platform to build complex biological systems interactively, and prepare simulation inputs with well-established and reproducible simulation protocols. While the modules in CHARMM-GUI are all functional, similar to most academic software, they have been developed by different students and postdocs, which requires substantial code cleaning and quality control to guarantee CHARMM-GUI's sustainable operations. So, this project will (AIM 1) maintain and Improve CHARMM-GUI and (AIM 2) improve Usability. This project also seeks to foster synergistic scientific research and education by providing a well-maintained, web-based cyberinfrastructure resource to students and researchers in multiple simulation communities for any general biomolecular simulations as well as advanced modeling and simulation.

研究生物分子如何随着时间的推移而变形的研究人员使用非常复杂的算法作为理解结构，运动和相互作用的不同方面的工具。这些工具是较大的软件应用程序的一部分，可捕获整个系统的行为，包括环境和生物分子中的原子和分子。随着研究人员对更大的组成部分建模更大的组成部分，超过较长的研究间隔，跟踪系统中的所有元素及其特性也已成为一个主要的障碍，即使对于相对经验丰富的计算生物学家也是如此。巨大的挑战是保持准确性和可重复性，同时有效地进行这些复杂的模拟以解决实际问题。该项目的目的是协助两类研究人员：知道如何设置条件并想要保存和分享它们的专家，以及需要指导来设置所有输入的非专家，也许有一些帮助解释结果。 Charmm-GUI已经解决了这些挑战，因为用户可以交互式设置复杂的生物分子系统，并可以轻松了解必须输入哪些文件才能进行最新的生物分子模拟。尽管有名称，但该界面不仅限于Charmm仿真软件包，而且还包括Gromacs，Amber，Genesis，Lammps，Desmond，OpenMM和Charmm/OpenMM。该项目旨在维护CHARMM-GUI接口应用程序的独特范围，同时改善代码库的一致性，使其更容易维护未来的工具，并使添加通过包括测试套件来正常工作的新功能更加易于工作。该项目的总体目标是帮助学生和研究人员进行创新和新颖的生物分子建模和模拟研究，以获取对生物分子感兴趣的生物分子系统的结构，动态和基本机制的新颖见解，可以通过出色的工具，具有良好的文档来维护该项目，以确保该项目的运作，以确保该项目的主要目标，以及一项项目的启用。（http://www.charmm-gui.org），基于Web的图形用户界面（GUI）。这将需要更改代码，以使其成为强大的，可持续的基于Web的网络基础架构，该结构支持广泛学科的专家和非专家用户，以轻松构建和模拟复杂的生物系统。在过去的10年中，Charmm-GUI证明，这种基于网络的GUI提供了一个理想的平台，可以交互作用地构建复杂的生物系统，并准备使用良好且可重复的模拟协议的模拟输入。尽管Charmm-GUI中的模块都具有功能，但类似于大多数学术软件，但它们是由不同的学生和博士后开发的，这需要大量的代码清洁和质量控制，以保证Charmm-GUI的可持续运营。因此，该项目将（AIM 1）维护和改善CHARMM-GUI和（AIM 2）提高可用性。该项目还旨在通过为任何一般的生物分子模拟以及高级建模和模拟的多个模拟社区的学生和研究人员提供基于网络的网络架构资源来促进协同的科学研究和教育。