SBEVSL -- Structural Biology Extensible Visualization Scripting Language

SBEVSL——结构生物学可扩展可视化脚本语言

• 批准号: 7827933
• 负责人: Herbert J. Bernstein
• 金额: $ 5.06万
• 依托单位: DOWLING COLLEGE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7827933
• 关键词: Adopted; Back; Bioinformatics; Boxing; Cartoons; Collection; Communication; Communities; Complement; Computer software; Databases; Devices; Dictionary; Drug Design; Elements; Environment; Extensible Markup Language; Goals; Hand; Hour; Image; Imagery; Individual; Internet; Investments; Java; Language; Learning; Libraries; Maps; Modeling; Modification; Molecular; Molecular Structure; Mus; Nomenclature; Ontology; Outcome; Principal Investigator; Process; Publications; Pythons; Reproducibility; Research; Research Infrastructure; Research Personnel; Resources; Software Tools; Solutions; Structural Biologist; Structure; System; Text; Time; Training; Translating; Translations; Work; Writing; abstracting; base; electron density; infrastructure development; meetings; movie; open source; programs; research study; structural biology; tool

DESCRIPTION (provided by applicant): The goal of the SBEVSL project is to create a new extensible scripting language for molecular graphics, as used in structural biology, by combining the intiutive expressive power of the widely used scripting language created by Roger Sayle for RasMol with the general object-oriented extensibility of the Python scripting of PyMOL. Major existing open source molecular graphics programs, including RasMol, Jmol and PyMol will be adapted to accept scripts written in the new scripting language. While it is fashionable and easy to work with GUI interfaces in controlling molecular graphics programs and to minimize the use of command line control, the saving of text files of commands from one program as scripts from which one can later reproduce images with a different program is an essential capability for scientific communication. In addition, use of command languages for visualization in structural biology yields precise control and reproducibility not obtainable by users with an ordinary pointing device such as a mouse or a dial box. There are many molecular graphics programs, most with their own command language and internal approach to storage of a database of structural elements, but for structural biology the conceptual framework to be supported is unified by the practical demands of structural biology. To be successful a molecular graphics program must provide a mechanism to select atoms, residues and chains and must be able to render wireframe, CPK, ball and stick, cartoon and other standard presentations. Rather than impose a language on any program, the SBEVSL project will extract all the concepts used in the command languages of major molecular graphics programs and gather them in one master ontology, using this essential dictionary as a relational database with GIF. Defining SBEVSL in terms of the dictionary and UML will allow expression of scripts in multiple formats so that SBEVSL can be widely used. This unification of an essential component of the infrastructure used in understanding and communicating the structure and function of biologically significant molecules will help to increase the efficiency of many activities in structural biology, such as drug design. Time now being lost in the struggle to move descriptions of molecular renderings among such programs as RasMol, Jmol, PyMOL, Molscript and Raster3D will become available for more productive activities.

描述（由申请人提供）：SBEVSL 项目的目标是通过将 Roger Sayle 为 RasMol 创建的广泛使用的脚本语言的直观表达能力与PyMOL 的 Python 脚本的一般面向对象可扩展性。现有的主要开源分子图形程序，包括 RasMol、Jmol 和 PyMol 将进行调整，以接受用新脚本语言编写的脚本。虽然使用 GUI 界面来控制分子图形程序并最大限度地减少命令行控制的使用是一种时尚且容易的做法，但将一个程序中的命令的文本文件保存为脚本，以便以后可以使用不同的程序重现图像是一种流行的做法。科学传播的基本能力。此外，使用命令语言进行结构生物学可视化可以实现用户使用鼠标或拨号盒等普通指点设备无法获得的精确控制和再现性。有许多分子图形程序，大多数都有自己的命令语言和结构元素数据库的内部存储方法，但对于结构生物学来说，要支持的概念框架是由结构生物学的实际需求统一的。为了获得成功，分子图形程序必须提供一种选择原子、残基和链的机制，并且必须能够渲染线框、CPK、球棒、卡通和其他标准演示。 SBEVSL 项目不会将一种语言强加于任何程序，而是提取主要分子图形程序的命令语言中使用的所有概念，并将它们收集在一个主本体中，使用这个基本字典作为 GIF 的关系数据库。从字典和UML的角度定义SBEVSL将允许多种格式的脚本表达，从而使SBEVSL得到广泛的应用。 这种用于理解和交流具有生物学意义的分子的结构和功能的基础设施的重要组成部分的统一将有助于提高结构生物学中许多活动的效率，例如药物设计。现在在 RasMol、Jmol、PyMOL、Molscript 和 Raster3D 等程序之间移动分子渲染描述的斗争中浪费的时间将可用于更具生产力的活动。