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INSPIRE: Systematic, scalable representation and simulation of whole-cell models

INSPIRE：全细胞模型的系统、可扩展的表示和模拟

基本信息

批准号：
1649014
负责人：
Jonathan Karr
金额：
$ 100万
依托单位：
Icahn School of Medicine at Mount Sinai
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2016
资助国家：
美国
起止时间：
2016-09-01 至 2020-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1649014&HistoricalAwards=false
关键词：
INSPIRE Systematic scalable representation simulation

项目摘要

This project is based on the concept that complex, living cells can be understood and described in terms of individual molecular interactions by using an integrated strategy. It makes use of a combination of diverse mathematics and computational approaches, that can deal with the many molecular components and interactions of a cell distributed in space and time. These models also have predictive power potentially identifying previously undetected biological functions. The long-term goal of this research is to develop detailed whole-cell computational models of all of the biochemical activities inside the cell. Such whole-cell models could transform many fields that rely on fundamental biological knowledge, including bioengineering, medicine, agriculture, energy and the environment. For example, it will enable bioengineers to rationally design whole organisms, and the medical field in developing personalized medical therapies. In addition, the tools developed will provide means for the early detection of diseases, decontamination of waste; production of better and cheaper fuels. and optimize critical industrial processes. The educational benefits at intersection of cellular systems biology, informatics and computer science is an excellent platform for creating an exceptionally well-trained future workforce.The primary goal of this project is to enable larger and more accurate whole-cell models by systemizing their representation and simulation. Toward this goal, the project will develop a novel high-level, data-driven, rule-based whole-cell modeling language and a physically accurate, scalable multi-algorithmic whole-cell simulator based on discrete event simulation. These tools will enable larger and more accurate models, and empower more researchers to engage in whole-cell modeling. In addition, the project will use this model to gain fundamental insights into single-cell metabolism. Part of the support will provide resource for the investigator to coordinate the whole-cell modeling community, through organizing whole-cell modeling meetings, develop whole-cell modeling tutorials, and train several students in this emerging and multi-disciplinary field.This is an INSPIRE award that was co-funded by the Office of integrative Activities (OIA), Biological Sciences Directorate, Division of Molecular and Cellular Biosciences (MCB), Systems and Synthetic Biology (SSB), and Cellular Dynamics and Functions (CDF) programs; and the Division of Biological Infrastructure (DBI), Advances in Biological Informatics (ABI) program; the Directorate for Mathematical & Physical Sciences (MPS) Division of Physics (PHY), the Physics Computing (PC) program; and the Directorate for Computer & Information Science & Engineering (CISE) Division of Computing and Communication Foundations (CCF) Algorithmic Foundations (AF) program.

这个项目是基于这样一个概念，即复杂的活细胞可以通过使用综合策略来理解和描述单个分子的相互作用。它利用不同的数学和计算方法的组合，可以处理分布在空间和时间上的细胞的许多分子成分和相互作用。这些模型还具有预测能力，有可能识别以前未被检测到的生物功能。这项研究的长期目标是开发详细的细胞内所有生化活动的全细胞计算模型。这种全细胞模型可以改变许多依赖基础生物学知识的领域，包括生物工程、医学、农业、能源和环境。例如，它将使生物工程师能够合理地设计整个生物体，并使医学领域能够开发个性化的医疗疗法。此外，所开发的工具将为及早发现疾病、清除废物污染、生产更好和更便宜的燃料提供手段。并优化关键工业流程。细胞系统生物学、信息学和计算机科学交叉的教育效益是创造一支训练有素的未来劳动力的极好平台。该项目的主要目标是通过系统化全细胞模型的表示和模拟来实现更大和更准确的全细胞模型。为了实现这一目标，该项目将开发一种新颖的高级、数据驱动、基于规则的全细胞建模语言和基于离散事件仿真的物理精确、可扩展的多算法全细胞仿真器。这些工具将使更大、更准确的模型成为可能，并使更多的研究人员能够从事全细胞建模。此外，该项目将使用这个模型来获得对单细胞新陈代谢的基本见解。部分支持将为研究人员提供资源，通过组织全细胞建模会议，开发全细胞建模教程，并在这个新兴的多学科领域培训几名学生。这是一个由综合活动办公室(OIA)、生物科学局、分子和细胞生物科学部(MCB)、系统和合成生物学(SSB)以及细胞动力学和功能(CDF)计划共同资助的INSPIRE奖；以及生物基础设施部(DBI)、生物信息学进展(ABI)计划；数学与AMP委员会；物理科学(MPS)物理部门(PHY)，物理计算(PC)计划；以及计算机与信息科学与工程委员会(CEISE)计算与通信基础(CCF)算法基础(AF)计划。