Integrative modeling of the cell

A whole-cell model represents certain aspects of the cell structure and/orfunction. Due to the high complexity of the cell, an integrative modeling approach is often taken to utilize all available information including experimental data, prior knowledge and prior models. In this review, we summarize an emerging workflow of whole-cell modeling into five steps: (i) gather information; (ii) represent the modeled system into modules; (iii) translate input information into scoring function; (iv) sample the whole-cell model; (v) validate and interpret the model. In particular, we propose the integrative modeling of the cell by combining available (whole-cell) models to maximize the accuracy, precision, and completeness. In addition, we list quantitative predictions of various aspects of cell biology from existing whole-cell models. Moreover, we discuss the remaining challenges and future directions, and highlight the opportunity to establish an integrative spatiotemporal multi-scale whole-cell model based on a community approach.

Automated summary

A whole-cell model is an integrative approach that represents certain aspects of the cell structure and/or function. This review summarizes the workflow of whole-cell modeling into five steps, including gathering information, representing the system into modules, translating input information into scoring function, sampling the whole-cell model, and validating and interpreting the model. By combining available models, the accuracy, precision, and completeness of the integrated cell model can be maximized. The review also discusses the quantitative predictions made by existing whole-cell models and highlights the challenges, future directions, and the opportunity for establishing a community-based integrative spatiotemporal multi-scale whole-cell model.