SeQuaiA

A Scalable Tool for Semi-Quantitative Analysis of Chemical Reaction Networks (CRNs)


Chemical reaction networks (CRNs) play a fundamental role in analysis and design of biochemical systems. They induce continuous-time stochastic systems, whose analysis is a computationally intensive task.

This tool implements the semi-quantitative analysis of CRN and offers:

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Basic Idea

The implemented approach is based on two steps. Firstly, a system abstraction is computed, where the states and transitions are abstracted by considering population ranges. Additionally, transitions are accelerated, taking segments of paths into account. The resulting models are small enough to allow for a synoptic observation of the model dynamics. Secondly, it performs semi-quantitative analysis, focusing on the most probable behaviours and more qualitative, global descriptions, such as oscillation, rather than fully quantitative sequences of exact transient distributions. This yields explainable models and is a sufficient and computationally cheaper technique.

Developer

SeQuaiA is developed and maintained by Milan Češka (Brno University of Technology), Jan Křetínský (Technical University of Munich) and Calvin Chau (Technical University of Munich).