Hands-on Workshops on Computational Biophysics

计算生物物理学实践研讨会

基本信息

批准号：
8414721
负责人：
Klaus Schulten
金额：
$ 16.45万
依托单位：
UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
依托单位国家：
美国
项目类别：
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/8414721
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 Learning Location Microscope Microscopic Minority Modeling Molecular Molecular Analysis Molecular Models Participant Process Recruitment Activity Research Personnel 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 lectures metropolitan molecular dynamics molecular modeling nanoscale parallel computer physical model programs public health relevance simulation tool web site

项目摘要

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）：计算技术提供了急需的细胞过程的显微镜视图，以遗传，结构和动态信息的形式出现。将这种越来越多的信息转化为健康相关策略，不仅需要适当的工具，而且还需要适当的培训。新概念的科学家 “计算显微镜”需要在使用分子建模和可视化软件工具中培训，而来自计算背景的人需要培训这些工具用于生物学问题。为此，我们提出了为期五天的计算生物物理学研讨会，介绍了大分子建模中心和生物信息学中心（CMMB）的广泛使用的软件。拟议的努力将利用CMMB在生物医学科学家培训中的经验，从720页的书面培训材料开始，这是一系列流行的动手讲习班。研讨会计划将在CMMB的软件程序，VMD（视觉分子动力学； 204,000个注册用户）和NAMD（纳米级分子动力学； 49,400个注册用户）中提供培训，并将其应用于科学询问。研讨会的参与者（通常是生命科学的实验和计算研究生和博士后伴侣）将探索用于模拟生物系统的物理模型和计算方法，并在原子水平上研究其功能。将引入相关的物理概念，数学技术和计算方法，包括用于分子建模中使用的力场和算法，平行计算机上的分子动力学模拟以及转导的分子动力学模拟。研讨会和评估数据中使用的更新的学习材料将随后传播到生物医学界。 CMMB试图每年举办三个动手研讨会，其家庭机构的一个当地研讨会，以及大都市大城市的两个壁外研讨会。