A Gene-Complete Computational Model of Yeast

酵母的基因完整计算模型

• 批准号: 8306941
• 负责人: Markus W Covert
• 金额: $ 79.2万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 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
• 来源: https://reporter.nih.gov/project-details/8306941
• 关键词: Accounting; Address; Aging; Biological; Biological Process; Biology; Cell division; Cell model; Cell physiology; Cells; Communities; Computer Simulation; DNA biosynthesis; Development; General Population; Genes; Lead; Life Cycle Stages; Longevity; Metabolism; Methods; Modeling; Online Systems; Protein Biosynthesis; RNA; Research Personnel; Scientist; Simulate; Testing; Transcriptional Regulation; Work; Yeasts; abstracting; cell type; implementation research; models and simulation; network models; programs; user-friendly; web interface

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.

抽象的 该提案的目标是建立一个可以模拟完整生命的计算模型 单个酵母细胞的循环，考虑到所有注释的基因，这被称为。 ¿理解简单细胞的终极考验¿并将彻底改变我们对生物学的看法 使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 我们将结合计算建模和之前的研究来证明这一点。 实验生物学，对衰老和寿命控制进行详细研究。 为了完成拟议的工作，必须解决一些智力挑战 例如，我们努力构建全细胞模型的一个主要组成部分将是。 依赖于大规模适用的新建模方法的开发。 此外，不同类型生物过程的模型整合方法， 每一个都可以使用不同的表示来最好地描述，这将是至关重要的。 P.I. 的特殊专长是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 ¿最终测试??建造全细胞计算机 模型，而是通过 用户友好的网络界面。该项目的一个交付成果是一个基于网络的平台。 将允许用户跟踪和干扰生物过程，例如 DNA 复制、RNA 对于科学家来说，转录和调节、蛋白质合成、代谢和细胞分裂。 平台将具有高级用户选项，以便其他研究人员可以调整我们的方法 无论他们喜欢哪种细胞类型，我们预计这都会导致广泛的实施。 使用计算建模和模拟来指导实验计划的研究 和生物学发现。