A New Simulation Engine

Biological sciences are experiencing an explosion of data, especially with the rise of single-cell omics. This wealth of information, from genomics, proteomics, metabolomics, and beyond, combined with with existing and expanding knowledge bases and graphs, offers incredible potential. However, understanding how all these pieces fit together and to extract meaningful and tractable information from this wealth of information remains a colossal challenge.

We think that digital modelization and simulation is key to tackle this challenge. At BioFi we developed the Endogenics Simulation Engine (ESE), a sophisticated platform designed to digitally model and simulate complex biological systems. It leverages cutting-edge mathematical and computational techniques to simulate biological processes with a level of detail and realism unmatched by traditional modeling.

The ESE provides a dynamic and data-driven way to account for key aspects of biological systems:

• Integrating diverse biological data
• Integrating biological networks like metabolism, gene regulation, signal transduction and more abstract physiological processes
• Capturing the stochastic and nonlinear nature of biology

At its heart, the ESE relies on a mathematical framework known as the master equation. This equation describes how a system’s state changes over time, capturing the probabilistic essence of biological events. Advanced numerical solvers allow us to evolve such biological events over time, even if they happen on different time scales.