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

项目摘要 十多年来，GLYCAM-Web(www.glcam.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 用蛋白质。低聚糖的高度可塑性以及它们通常是分支的事实意味着 他们对软件开发人员和用户都提出了独特的要求。他们的情结加剧了这一点 和陈旧的命名法。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，首要目标是制造碳水化合物 缺乏计算专业知识或熟悉以下方面的科学家更容易使用建模 碳水化合物是有限的。 根据AWSTATS和内部代码，GLYCAM-Web被大约110,000个唯一地址访问，并具有 从2016年到2019年，大约11,000次PDB文件下载。下载通常与创建和 查看多糖的3D结构并用于离线建模。中包含了详细的使用情况分析。 研究战略，强调这一资源对NIGMS研究社区的重要性。 GLYCAM-WEB的开发主要由NIH NIGMS P41赠款支持，该赠款在 佐治亚大学复合碳水化合物研究中心不断更新 自20世纪90年代以来。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，使我们能够将GLYCAM-Web过渡到几乎自给自足的 其运营成本被新的按服务收费功能抵消的资源，目标用户希望 进行分子动力学模拟，但缺乏这样做的专业知识或基础设施的人。这十年- GLYCAM-Web的长期发展见证了基础设施的发展和新技术的出现 架构、代码演变和更高的安全要求，导致复杂的代码库，包括 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，将直接降低维护成本。为了实现近乎自我可持续发展，我们 我制定了四个目标，将解决对代码和基础设施的必要改进： 可用性、可转移性、可维护性和可持续性。

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.