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.
