Resource for Macromolecular Modeling and Visualization

高分子建模和可视化资源

• 批准号: 10431033
• 负责人: Emad Tajkhorshid
• 金额: $ 120.73万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-28 至 2027-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10431033
• 关键词: Algorithms; Area; Automation; Bioinformatics; Biological; Biomedical Research; Biomedical Technology; COVID-19; Case Study; Cell model; Cells; Cloud Computing; Code; Collection; Communities; Computational algorithm; Computer Models; Computer software; Consumption; Cryoelectron Microscopy; Custom; Data Collection; Documentation; Educational workshop; Emerging Technologies; Ensure; Free Energy; Funding; Genome; Goals; Illinois; Image; Individual; Industry; Institution; Internet; Knowledge; Ligands; Mainstreaming; Medicine; Membrane Proteins; Methods; Mission; Modeling; Modernization; Molecular; Monitor; Monoclonal Antibody R24; National Center for Research Resources; National Institute of General Medical Sciences; Performance; Positioning Attribute; Prize; Procedures; Protein Dynamics; Reproducibility; Research; Research Personnel; Resources; Running; Sampling; Science; Scientist; Services; Software Tools; Structural Biologist; Supercomputing; Surveys; System; Techniques; Technology; Time; Training; Training Activity; Training Programs; Training Support; United States National Institutes of Health; Update; Vendor; Visit; Visualization; Work; base; biomedical scientist; computational platform; computerized tools; cost; cyber security; data quality; empowered; experience; interoperability; laptop; large datasets; models and simulation; molecular modeling; online tutorial; operation; outreach; programs; screening; simulation; software development; structural biology; supercomputer; tool; user friendly software; web server; web site

SUMMARY The main mission of the P41 Biomedical Technology Research Resource for Macromolecular Modeling and Bioinformatics (P41-GM104601) over the last three decades has been developing state of the art computational technologies for biomolecular and cell simulations and visualization, implementing them in efficient, economical, user-friendly software solutions, and disseminating them to the biomedical community at no cost. The Resource has enabled high-quality, rigorous research for the biomedical scientists who need to integrate molecular and cell modeling, simulation, and visualization in their research, not only at diverse academic institutions, but also in industry. The flagship software programs, VMD and NAMD and their auxiliary plugins, are used currently by more than 125,000 users and have received a staggering number of 57,000 citations (19,711 in 2018-2021 alone), reflecting the massive use of the technologies and programs developed by the Resource, and its sub- stantial economies of scale. The Resource's partnership with the biomedical community resulted in the 2020 ACM Gordon Bell Special Prize for COVID-19 Research. Under the R24 mode of operation, a major goal of the Resource will be to ensure that its software solutions remain current and available to its large user base on existing and upcoming hardware platforms commonly used at local and institutional levels, and at national super- computing centers, where a large fraction of the overall time is consumed by biomedical researchers using the Resource's programs. Given the key position of these programs, several major supercomputing centers as well as major hardware vendors have established strong relationships with the Resource, even directly supporting software development and optimization. In addition, the Resource will ensure the utility of its programs by includ- ing algorithmic changes/updates that are critical to applicability of the codes and/or demanded by the community. The Resource will also sustain and expand its comprehensive user training program, empowered by an already existing, large collection of online tutorials, case studies, and hands-on workshops. Another major activity of the Resource will be to continue to support its users in the proper and efficient application of the software programs through customer support services and expanding and upgrading the documentation for the programs. The R24 Resource for Macromolecular Modeling and Visualization will be evaluated on a continuous basis by monitoring quantitative metrics such as the number of its active users (users of multiple versions of software) and citations, by conducting regular user surveys requesting input from the user community which will also assist in identifying most critical features and improvements, and by the technical input from the external advisory board.

摘要 P41生物医学技术研究资源的主要任务是大分子建模和 生物信息学(P41-GM104601)在过去的三十年里一直在发展最先进的计算机 用于生物分子和细胞模拟和可视化的技术，在高效、经济、 用户友好的软件解决方案，并免费向生物医学界传播。《资源》 为生物医学科学家提供了高质量、严谨的研究，他们需要将分子和 细胞建模、模拟和可视化的研究，不仅在不同的学术机构，而且 在工业上。目前使用的是fl代理软件程序vmd和namd及其辅助插件 超过125,000名用户，并收到了惊人的57,000条引文(2018-2021年为19,711条 单独)，fl资源开发的技术和程序的大量使用，以及其子 持续的规模经济。该资源与生物医学界的合作伙伴关系导致2020年 ACM戈登·贝尔新冠肺炎研究特别奖。在R24运行模式下，主要目标是 该资源将确保其软件解决方案保持最新，并可供其庞大的用户群使用 现有和即将推出的硬件平台通常用于地方和机构级别，以及国家超级 计算中心，在那里，生物医学研究人员使用 资源的程序。鉴于这些程序的关键地位，几个主要的超级计算中心也 由于主要硬件供应商已与该资源建立了牢固的关系，甚至直接支持 软件开发和优化。此外，资源还将通过以下方式确保其方案的效用： 对代码适用性和/或社区要求至关重要的ING算法更改/更新。 该资源还将维持和扩大其全面的用户培训计划，该计划由一个已经 现有的大量在线教程、案例研究和实践研讨会。另一项主要活动是 资源将继续支持其用户正确和有效地应用软件程序 通过客户支持服务以及扩展和升级计划的文档。R24 将通过监测持续评估用于大分子建模和可视化的资源 诸如其活跃用户(多个软件版本的用户)的数量和引用等定量指标， 通过定期进行用户调查，请求用户社区提供意见，这也将有助于确定 最关键的特点和改进，以及外部咨询委员会的技术投入。