SeQuaiA: A Scalable Tool for Semi-Quantitative Analysis of Chemical Reaction Networks

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. We present a tool that implements the recently proposed semi-quantitative analysis of CRN. Compared to the proposed theory, the tool implements the analysis so that it is more flexible and more precise. Further, its GUI offers a wide range of visualization procedures that facilitate the interpretation of the analysis results as well as guidance to refine the analysis. Finally, we define and implement a new notion of “mean” simulations, summarizing the typical behaviours of the system in a way directly comparable to standard simulations produced by other tools.