Extending BioD to Describe Gene Regulation

扩展 BioD 来描述基因调控

• 批准号: 6416518
• 负责人: DANIEL L COOK
• 金额: $ 8.82万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-03-01 至 2004-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6416518
• 关键词: bacterial virus; biotechnology; cell biology; computer data analysis; computer graphics /printing; computer program /software; computer simulation; computer system design /evaluation; functional /structural genomics; gene expression; genetic regulation; lysogeny; mathematical model; molecular biology; molecular genetics

DESCRIPTION (provided by applicant): We have proposed that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. Toward this we suggest a conceptual basis for designing such a language and describe BioD, a prototype language that we have used to explore the utility and feasibility of this approach to functional biology. Using example models, we demonstrate that a rather limited lexicon of icons and arrows suffices to describe complex cell biological systems as discrete models that can be posted and linked on the internet. Given available computer and internet technology, we also suggest that BioD may be implemented as an extensible, multidisciplinary language that can be used to archive functional systems knowledge and be extended to support both qualitative and quantitative functional analysis. In this application, we propose to test three critical assertions about the BioD language approach using the lambda phage lysis/lysogeny "genetic switch" as a classical, well characterized test case. First, we want to determine whether the BioD language can be extended to comprehensively describe gene regulation and expression mechanism found in the lambda phage genetic switch. Second, we aim to determine whether the BioD icon and arrow objects in the lambda phage system can be rigorously mapped to computational expressions for simulating model behavior. And third, we aim to establish the framework and basic patterns of a novel BioD Functional Pattern Language for defining, identifying and analyzing higher-order principles of organization of biological systems as an aid to understanding cell biological and genetic function.

描述（由申请人提供）：我们提出了一个计算机化， 基于Internet的图形描述系统生物学的语言将是 描述，归档和分析复杂问题至关重要 健康和疾病中的生物学功能。在此方面，我们建议一个概念 设计这种语言并描述Biod，一种原型语言的基础 我们用来探索这种方法的实用性和可行性 功能生物学。使用示例模型，我们证明了一个相当有限的 图标和箭头的词典足以描述复杂的细胞生物学 可以在Internet上发布和链接的离散模型的系统。给出 可用的计算机和互联网技术，我们还建议Biod可能是 作为一种可扩展的多学科语言实现 存档功能系统知识并扩展以支持 定性和定量功能分析。在此应用程序中，我们 建议测试有关BIOD语言方法的三个关键主张 使用lambda噬菌体裂解/裂解性“遗传开关”作为经典，很好 特征测试案例。首先，我们要确定Biod语言是否 可以扩展以全面描述基因调节和表达 在Lambda噬菌体遗传转换中发现的机制。第二，我们旨在确定 lambda噬菌体系统中的生物编号图标和箭头对象是否可以是 严格映射到计算表达式以模拟模型行为。 第三，我们旨在建立一种新型生物制的框架和基本模式 用于定义，识别和分析的功能模式语言 生物系统组织组织的高阶原则作为帮助 了解细胞生物学和遗传功能。