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创新表达能力与PyMOL的Python脚本的一般面向对象的可扩展性相结合，为结构生物学中使用的分子图形创建一种新的可扩展脚本语言。现有的主要开源分子图形程序，包括RasMol、Jmol和PyMol，将被修改以接受用新的脚本语言编写的脚本。虽然在控制分子图形程序中使用GUI界面和最小化命令行控制的使用是流行和容易的，但是将来自一个程序的命令的文本文件保存为脚本，稍后可以用不同的程序再现图像，这是科学交流的基本能力。此外，在结构生物学中使用命令语言进行可视化产生了用户使用普通指向设备（如鼠标或拨号盒）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内部方法来存储结构元素的数据库，但对于结构生物学，要支持的概念框架是由结构生物学的实际需求统一的。要成功的分子图形程序必须提供一个机制来选择原子，残基和链，必须能够渲染线框，CPK，球和棒，卡通和其他标准的演示。SBEVSL项目不是在任何程序上强加一种语言，而是将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。根据字典和UML定义SBEVSL将允许以多种格式表达脚本，以便SBEVSL可以被广泛使用。 这种用于理解和交流生物学重要分子的结构和功能的基础设施的基本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富有成效的活动。