Continued Development and Maintenance of GLYCAM-Web

描述(申请人提供)：碳水化合物修饰蛋白质和细胞表面，作为疾病和免疫过程的识别实体，与细胞衰老有关，并用作生物信号载体。它们在许多方面都很有用的一个原因是，它们可以采用令人震惊的各种形状。部分是因为它们对生物系统的重要性，部分是因为它们的结构复杂性，因此至关重要的是，科学家，特别是那些研究它们的生物角色的科学家，能够轻松地生成它们及其与蛋白质的复合体的准确和有用的3D模型。然而，由于碳水化合物结构的复杂性，这些模型的生成非常困难。即使是熟悉生物系统计算机建模的研究人员也会发现，这项任务令人望而生畏。然而，仅仅促进计算专家的准确建模是不够的。为了克服广泛的研究人员采用这种方法的障碍，重要的是该软件具有直观性，并提供适当使用的指导。GLYCAM-Web在线工具套件(www.glcam.org)多年来一直在朝着这一目标迈进。六年前，它开始是伍兹碳水化合物建模研究小组的内部工具。不久之后，它以免费在线实用程序的形式公开发布。网站统计数据已经收集了大约5年，平均每个月的访问量为400-500次。根据支持请求、征求用户信函和在学术期刊中找到的对该网站的引用，它主要由从事生物研究的人员使用。该网站最初的设计并不是为了这样的扩张，也不是为了让如此广泛的研究人员使用。该项目的目的是将GLYCAM-Web建模工具套件更新和转换为能够满足当前和未来糖生物学研究需求的稳定、健壮、信息丰富和直观的实用工具。为了实现这些目标，网站的软件将进行重组，以使其由易于维护和修改的自含式、经过良好测试的模块构建。它的数据结构将有助于添加新功能。为了使外部研究人员能够在当地使用该软件并对其进行修改以满足他们的需要，将向公众发布建立该网站的命令行界面。将鼓励用户社区提交和更正。为了使网站可供更多的研究人员使用，特别是那些主要不是计算机科学家的研究人员，将增加或增强几项功能，并将根据用户的要求大大扩展网站文档。要增加或增强的功能包括更智能的错误检查、复杂结构的简化构建、更多支持的文件格式以及与外部网站的接口。 与公共健康相关：碳水化合物在人类健康中扮演着许多角色，除了在营养方面更广为人知的角色外，还参与免疫反应和细胞老化等过程。然而，与蛋白质不同，碳水化合物形成高度分枝和异质结构，这使得它们的实验分析具有独特的挑战性。计算方法有机会通过提供可靠的模型来帮助理解它们的3D属性。该项目的目标是改进已被证明有助于碳水化合物建模的现有软件，使其更稳定、更具可扩展性，并可供从事与健康相关研究的科学家使用，但他们不一定是计算机建模专家。

DESCRIPTION (provided by applicant): Carbohydrates decorate proteins and cell surfaces serving as recognition entities for disease and immune processes, are implicated in cell aging and are used as biological signal carriers. One reason they are useful in so many ways is that they can adopt a staggering variety of shapes. Partly because of their importance to biological systems, and partly because of their structural complexity, it is critical that scientists, especially those studying their biological roles, be able easily to generate accurate and useful 3D models of them and their complexes with proteins. However, because of the structural complexity of carbohydrates, generation of these models is very difficult. Even researchers who are comfortable with computer modeling of biological systems can find the task daunting. It is not sufficient, however, only to facilitate accurate modeling for computational specialists. In order to overcome the barrier to adoption of such methods by a broad base of researchers, it is important that the software be intuitive and provides guidance in appropriate use. The GLYCAM-Web suite of online tools (www.glycam.org) has been making steps toward this goal for a number of years. Six years ago, it began as an in-house tool for the Woods carbohydrate modeling research group. Shortly thereafter it was released publically as an online utility free of charge. Site statistics have been gathered for approximately 5 years, and typically averages 400-500 visits each month. Based on support requests, solicited user letters, and references to the site found in academic journals, it is primarily used by persons engaged in biological research. The site was not initially designed with the anticipation of such expansion, nor was it initially intended for such a wide base of researchers. The purpose of this project is to update and transform the GLYCAM-Web suite of modeling tools into a stable, robust, informative and intuitive utility that is capable of meeting the current and future needs of glycobiology research. To achieve these goals, the site's software will be restructured so that it is built of self-contained, well-tested modules that are easy to maintain and modify. Its data structure will facilitate the addition of new functionality. To enable external researchers to use the software locally and modify it to meet their needs, the command-line interface on which the site is built will be released to the public. Submissions and corrections from the user community will be encouraged. To make the site usable by a wider variety of researchers, notably that are not primarily computer scientists, several features will be added or enhanced and site documentation will be greatly expanded based on user requests. Among the features to be added or enhanced are smarter error- checking, simplified builds of complex structures, an increased number of supported file formats, and interfaces with external web sites. PUBLIC HEALTH RELEVANCE: Carbohydrates serve many roles in human health, being involved in processes such as immune response and cell aging in addition to their better-known roles in nutrition. However, unlike proteins, carbohydrates form highly branched and heterogeneous structures, making their experimental analysis uniquely challenging. Computational methods have an opportunity to help in understanding their 3D properties by providing reliable models. The goal of this project is to improve existing software already shown to facilitate carbohydrate modeling, making it more stable, extensible and usable by scientists doing health-related research but who are not necessarily computer modeling experts.