A Gene-Complete Computational Model of Yeast

酵母的基因完整计算模型

基本信息

批准号：
7939721
负责人：
Markus W Covert
金额：
$ 80万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-30 至 2014-07-31
项目状态：
已结题

项目摘要

DESCRIPTION Abstract The target of this proposal is to build a computational model that can simulate a complete life cycle of a single yeast cell, taking into account all of the annotated genes. This has been called "the ultimate test of understanding a simple cell" and will revolutionize how we view biology, by allowing us to examine interactions between major cellular processes which have never been studied before. We will demonstrate this point, integrating computational modeling and experimental biology, in a detailed study of aging and lifespan control. Several intellectual challenges will have to be addressed to complete the proposed work successfully. For example, a major component of our effort to build a whole-cell model will depend on the development of new modeling approaches, applicable at a large scale. Additionally, methods for the integration of models for different types of biological processes, each of which may be best described using different representation, will be critical. Fortunately, the particular expertise of the P.I. is in modeling a variety of cellular processes, and in particular integrating different network models at the large scale. Our proposed work aims not only to pass the "ultimate test" of building a whole-cell computer model, but to make it accessible to the scientific community and the general public through a user-friendly web interface. One deliverable of the project will be a web-based platform which will allow the user to track and perturb biological processes such as DNA replication, RNA transcription and regulation, protein synthesis, metabolism and cell division. For scientists, the platform will have advanced user options, so that other researchers can adapt our methods to whichever cell type(s) they prefer. We anticipate that this could lead to a broad implementation of research which uses computational modeling and simulation to guide experimental programs and biological discovery. Public Health Relevance The broad goal of this res

描述抽象的该提案的目标是建立一个计算模型，可以模拟单个酵母细胞的完整生命周期，并考虑所有注释的基因。这被称为“理解简单细胞的终极测试”，并将彻底改变我们看待生物学的方式，让我们能够检查以前从未研究过的主要细胞过程之间的相互作用。我们将在衰老和寿命控制的详细研究中结合计算模型和实验生物学来证明这一点。为了成功完成拟议的工作，必须解决一些智力挑战。例如，我们建立全细胞模型的努力的一个主要组成部分将取决于大规模适用的新建模方法的开发。此外，不同类型的生物过程的模型整合方法将至关重要，每个生物过程都可以使用不同的表示来最好地描述。幸运的是，P.I. 的特殊专业知识。正在对各种细胞过程进行建模，特别是大规模集成不同的网络模型。我们提出的工作不仅旨在通过构建全细胞计算机模型的“终极测试”，而且旨在通过用户友好的网络界面使其可供科学界和公众使用。该项目的一项交付成果将是一个基于网络的平台，该平台将允许用户跟踪和干扰生物过程，例如 DNA 复制、RNA 转录和调节、蛋白质合成、新陈代谢和细胞分裂。对于科学家来说，该平台将具有高级用户选项，以便其他研究人员可以根据他们喜欢的细胞类型调整我们的方法。我们预计这可能会导致使用计算建模和模拟来指导实验计划和生物发现的研究的广泛实施。公共卫生相关性本研究的总体目标