Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

Highlights•Microbial cell factories are becoming important in sustainable chemical
production.•Systems metabolic engineering allows efficient microbial cell factory …

The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's
components with atomic resolution. In contrast to their real-world counterparts …

Background Kinetic models of biochemical systems usually consist of ordinary differential
equations that have many unknown parameters. Some of these parameters are often …

Over the last two decades, thousands of genome-scale metabolic network models (GSMMs)
have been constructed. These GSMMs have been widely applied in various fields, ranging …

Dynamical systems describing whole cells are on the verge of becoming a reality. But as
models of reality, they are only useful if we have realistic parameters for the molecular …

Agent-based modelling has proven its usefulness in several biomedical projects by
explaining and uncovering mechanisms in diseases. Nevertheless, the scenarios addressed …

Whole-cell dynamical models of human cells are a central goal of systems biology. Such
models could help researchers understand cell biology and help physicians treat disease …

Comprehensive data about the composition and structure of cellular components have
enabled the construction of quantitative whole-cell models. While kinetic network–type …

Highlights•Whole-cell models predict phenotype from genotype by representing each gene
function.•Whole-cell models could transform bioscience, bioengineering, and …