Gene regulatory networks modeling
Computational modeling is an important tool to better understand the complex behavior and nonintuitive feedback loops in gene regulatory networks. However, specialized modeling terminology is often a barrier to communication.
The researchers in this publication present a glossary for biologists of terms associated with modeling gene regulatory networks, such as Boolean networks, Petri nets, or differential equations.
Models can capture complex network behavior, such as cooperativity in the binding of proteins, bistability, where the network behaves like an on/off switch, and hysteresis, in which the history of the system influences the outcome.
Likewise, models can be formulated to take into account the stochasticity or probabilistic nature of molecular interactions.
Finally, simulation of reaction–diffusion models can generate patterns de novo (e.g., of cell types or pigments).
https://www.cell.com/trends/plant-science/fulltext/S1360-1385(26)00027-0
