Extending BioD to Describe Gene Regulation

描述(由申请人提供)：我们已经提出了一个计算机化的， 基于互联网的系统生物学图形描述语言将是 描述、归档和分析复杂问题的基本要素 在健康和疾病中的生物功能。对此，我们建议一个概念性的 设计这样一种语言的基础和描述原型语言BioD 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，我们演示了一个相当有限的 图标和箭头的词典足以描述复杂的细胞生物学 系统作为离散的模型，可以在互联网上发布和链接。vt.给出 可用的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 归档功能系统知识，并可扩展以支持两者 定性和定量的功能分析。在此应用程序中，我们 建议测试关于BioD语言方法的三个关键断言 利用Lambda噬菌体裂解/溶源“遗传开关”作为经典的 特性化的测试用例。首先，我们想确定BioD语言是否 可以扩展到全面描述基因的调控和表达 在Lambda噬菌体遗传开关中发现的机制。第二，我们的目标是确定 Lambda噬菌体系统中的BioD图标和箭头对象是否可以 已严格映射到用于模拟模型行为的计算表达式。 第三，我们的目标是建立一个新的BioD的框架和基本模式 用于定义、识别和分析的函数模式语言 生物系统组织的更高阶原则作为辅助 了解细胞生物学和遗传功能。

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.