Transitioning GLYCAM-Web to a self-sustaining carbohydrate modeling service

将 GLYCAM-Web 转变为自我维持的碳水化合物建模服务

• 批准号: 10391344
• 负责人: ROBERT J WOODS
• 金额: $ 41.53万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10391344
• 关键词: Address; Antibodies; Architecture; Automation; Biotechnology; Carbohydrate Chemistry; Carbohydrates; Chemistry; Code; Communities; Complex; Computer software; Development; Docking; Documentation; Engineering; Ensure; Environment; Evolution; Familiarity; Fee-for-Service Plans; Fees; Glycoproteins; Goals; Grant; Head; Human Resources; Informatics; Infrastructure; Internet; Language; Libraries; Longevity; Maintenance; Modeling; Monoclonal Antibody R24; National Institute of General Medical Sciences; Nature; Nomenclature; Oligosaccharides; Persons; Polysaccharides; Proteins; Publications; Research; Research Activity; Resources; Scientist; Security; Service delivery model; Services; Site; Solid; Specificity; Structure; System; Testing; United States National Institutes of Health; Universities; Visit; Wood material; base; carbohydrate binding protein; carbohydrate structure; cost; improved; interoperability; molecular dynamics; operation; pressure; programs; response; statistics; success; sustainable resource; three dimensional structure; three-dimensional modeling; tool; usability; web site

Project Summary For over a decade, GLYCAM-Web (www.glycam.org) has provided the scientific community with a suite of online tools for simplifying the modeling of 3D structures of carbohydrates, glycoproteins, and their interactions with proteins. The highly plastic nature of oligosaccharides and the fact that they are typically branched means that they place unique demands on both software developers and users. This is exacerbated by their complex and archaic nomenclature. GLYCAM-web was developed by a team of people with a unique depth of expertise in carbohydrate chemistry and informatics, with the overarching goal of making carbohydrate modeling more accessible to scientists who either lack computational expertise, or whose familiarity with carbohydrates is limited. According to AWstats and in-house code GLYCAM-Web was visited by ~110,000 unique addresses and had ~11,000 PDB file downloads from 2016 to 2019. The downloads are usually associated with creating and viewing 3D structures of glycans and for offline modeling. We have included a detailed usage analysis in the Research Strategy to emphasize the significance of this resource to the NIGMS research community. The development of GLYCAM-Web has been primarily supported through an NIH NIGMS P41 grant held at the Complex Carbohydrate Research Center at the University of Georgia that has been continuously renewed since the 1990s. With the ending of the P41 program, we are not eligible for further support within the P41 program, and are seeking support that with enable us to transition GLYCAM-Web to a near self-sustaining resource whose operation costs are offset by new fee-for-service functionality targeting users who wish to perform molecular dynamics simulations, but who lack the expertise or infrastructure to do so. The decade- long development of GLYCAM-Web has seen the infrastructure grow and change with the advent of new architectures, code evolution, and increased security requirements, leading to a complex code base involving the C++, JAVA, and PYTHON languages. Thus a significant aspect of this proposal involves code refactoring to unify the code base, which will directly reduce maintenance costs. To achieve near self-sustainability, we have developed the four aims what will address the necessary improvements to code and infrastructure: usability, transferability, maintainability, and sustainability.

项目摘要 十多年来，GLYCAM-Web（www.glycam.org）为科学界提供了一套 用于简化碳水化合物、糖蛋白及其相互作用的3D结构建模的在线工具 蛋白质。寡糖的高度可塑性和它们通常是支链的事实意味着 他们对软件开发人员和用户都提出了独特的要求。这是加剧了他们的复杂 和古老的命名法GLYCAM-web是由一个具有独特深度的团队开发的， 碳水化合物化学和信息学方面的专业知识，其总体目标是使碳水化合物 建模更容易被缺乏计算专业知识或熟悉 碳水化合物有限。 根据AWstats和内部代码，GLYCAM-Web被约110，000个唯一地址访问， 从2016年到2019年，约有11，000个PDB文件下载。下载通常与创建和 查看聚糖的3D结构和离线建模。我们已在 研究战略强调这一资源对NIGMS研究界的重要性。 GLYCAM-Web的开发主要是通过NIH NIGMS P41赠款支持的， 格鲁吉亚大学复杂碳水化合物研究中心，该中心不断更新 从90年代开始随着P41计划的结束，我们没有资格在P41中获得进一步的支持 计划，并正在寻求支持，使我们能够过渡GLYCAM-Web到一个接近自我维持 一种资源，其运营成本被新的服务收费功能所抵消，该功能针对希望 执行分子动力学模拟，但缺乏专业知识或基础设施这样做。十年- GLYCAM-Web的长期发展见证了基础设施的增长和变化， 体系结构、代码演进和不断增加的安全需求，导致代码库变得复杂， C++、JAVA和PYTHON语言。因此，该提案的一个重要方面涉及代码重构 统一代码库，这将直接降低维护成本。为了实现自我可持续发展，我们 制定了四个目标，以解决代码和基础设施的必要改进： 可用性、可移植性、可维护性和可持续性。