Hands-on Workshops on Computational Biophysics

计算生物物理学实践研讨会

• 批准号: 9135484
• 负责人: Emad Tajkhorshid
• 金额: $ 13.97万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-27 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9135484
• 关键词: Algorithms; Area; Bioinformatics; Biological; Biological Sciences; Biophysics; Cell physiology; Clinical Research; Communities; Computational Biology; Computer Simulation; Computer software; Computing Methodologies; Data; Educational workshop; Evaluation; Event; Extramural Activities; Genetic; Health; Home environment; Imagery; Institution; Investigation; Laboratory Study; Location; Microscope; Microscopic; Modeling; Molecular; Molecular Analysis; Molecular Models; Participant; Process; Recruitment Activity; Research Personnel; Scientific Inquiry; Scientist; Series; Slide; Software Tools; Techniques; Technology; Training; Translating; Update; Videotape; Visual; Visualization software; Writing; base; biological systems; biomedical scientist; computerized tools; experience; graduate student; learning materials; lectures; metropolitan; minority scientist; molecular dynamics; molecular modeling; nanoscale; parallel computer; physical model; programs; simulation; tool; web site

DESCRIPTION (provided by applicant): Computational technologies provide much needed microscopic views of cellular processes, coming in the form of genetic, structural, and dynamic information. Translating this ever growing amount of information into health relevant strategies requires not only the proper tools, but also the proper training. Scientists new to the notion of a "computational microscope" need training in the use of molecular modeling and visualization software tools, while those from a computational background need training in the application of the tools to biological problems. To this end, we propose five-day computational biophysics workshops introducing the widely used software of the Center for Macromolecular Modeling and Bioinformatics (CMMB). The proposed effort will take advantage of the CMMB's experience in the training of biomedical scientists, starting from over 720 pages of written training material an a past series of popular hands-on workshops. The program of the workshops will provide training in the CMMB's software programs, VMD (visual molecular dynamics; 204,000 registered users) and NAMD (nanoscale molecular dynamics; 49,400 registered users), and their application to scientific inquiries. Workshop participants (typically experimental and computational graduate students and postdoctoral associates in the life sciences) will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations. Updated learning materials used in the workshops and evaluation data will be subsequently disseminated to the biomedical community. The CMMB seeks to host three hands-on workshops per year, one local workshop at its home institution, and two extramural workshops in large metropolitan areas.

描述（由申请人提供）：计算技术以遗传、结构和动态信息的形式提供了急需的细胞过程的微观视图。将不断增加的信息转化为健康相关策略不仅需要适当的工具，还需要适当的培训。科学家们对“a”的概念还很陌生 “计算显微镜”需要接受分子建模和可视化软件工具使用方面的培训，而具有计算背景的人员则需要接受将这些工具应用于生物问题的培训。为此，我们建议举办为期五天的计算生物物理学研讨会，介绍高分子建模和生物信息学中心（CMMB）广泛使用的软件。拟议的工作将利用 CMMB 在生物医学科学家培训方面的经验，从超过 720 页的书面培训材料和过去一系列受欢迎的实践研讨会开始。讲习班的计划将提供有关 CMMB 软件程序、VMD（视觉分子动力学；204,000 名注册用户）和 NAMD（纳米级分子动力学；49,400 名注册用户）及其在科学探究中的应用的培训。研讨会参与者（通常是生命科学领域的实验和计算研究生和博士后）将探索用于模拟生物系统及其在原子水平上的功能研究的物理模型和计算方法。将介绍相关的物理概念、数学技术和计算方法，包括分子建模中使用的力场和算法、并行计算机上的分子动力学模拟和引导分子动力学模拟。研讨会中使用的更新学习材料和评估数据随后将分发给生物医学界。 CMMB 力求每年举办三场实践研讨会，在其所在机构举办一场本地研讨会，以及在大城市地区举办两场校外研讨会。