Extending BioD to Describe Gene Regulation

描述（由申请人提供）：我们提出了一个计算机化的， 基于因特网系统生物学图形描述语言将 对于描述、归档和分析复杂的 健康和疾病的生物学功能。为此，我们提出了一个概念性的 设计这种语言的基础，并描述了BioD，一种原型语言 我们已经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 图标和箭头的词汇足以描述复杂的细胞生物学 系统作为离散的模型，可以在互联网上发布和链接。给定 利用计算机和互联网技术，我们还建议BioD可能是 实现为可扩展的多学科语言，可用于 存档功能系统知识，并扩展以支持 定性和定量功能分析。在本申请中，我们 我建议测试关于BioD语言方法的三个关键断言 使用λ噬菌体裂解/溶源性“遗传开关”作为经典的， 特征测试用例。首先，我们要确定BioD语言是否 可以扩展到全面描述基因调控和表达 在λ噬菌体基因开关中发现的机制。第二，我们的目标是确定 λ噬菌体系统中的BioD图标和箭头对象是否可以 严格映射到用于模拟模型行为的计算表达式。 第三，建立了一个新的生物多样性的框架和基本模式 用于定义、识别和分析的功能模式语言 生物系统组织的高阶原理， 了解细胞的生物学和遗传学功能。

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.