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.

概括 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技术 生物分子和细胞模拟和可视化技术，以高效、经济、 用户友好的软件解决方案，并将其免费传播给生物医学界。资源 为需要整合分子和分子生物学的生物医学科学家提供了高质量、严谨的研究 他们的研究中的细胞建模、模拟和可视化，不仅在不同的学术机构，而且在 在工业中。目前使用的旗舰软件程序VMD和NAMD及其辅助插件 受到超过 125,000 名用户的关注，并获得了惊人的 57,000 次引用（2018-2021 年为 19,711 次） 单独），反映了资源及其子项目开发的技术和程序的大量使用 显着的规模经济。该资源与生物医学界的合作导致了 2020 年 ACM 戈登贝尔 COVID-19 研究特别奖。在R24运作模式下，一个主要目标是 该资源将确保其软件解决方案保持最新状态并可供其庞大的用户群使用 地方和机构层面以及国家超级市场普遍使用的现有和即将推出的硬件平台 计算中心，其中大部分时间都被生物医学研究人员使用 资源的程序。鉴于这些项目的关键地位，几个主要的超级计算中心也 由于主要硬件供应商与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，该资源将通过以下方式确保其计划的实用性： 对代码的适用性和/或社区要求至关重要的算法更改/更新。 该资源还将维持和扩大其全面的用户培训计划，由已经存在的 现有的大量在线教程、案例研究和实践研讨会。本次活动的另一项重大活动 资源将继续支持用户正确有效地应用软件程序 通过客户支持服务以及扩展和升级程序文档。 R24 将通过监测持续评估大分子建模和可视化资源 定量指标，例如活跃用户数量（多个版本软件的用户）和引用次数， 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 最关键的功能和改进，以及外部顾问委员会的技术投入。