Catalyst: Fast and flexible modeling of reaction networks

Torkel E. Loman, Yingbo Ma, Vasily Ilin, Shashi Gowda, Niklas Korsbo, Nikhil Yewale, Chris Rackauckas, Samuel A. Isaacson

Abstract: Author summary Chemical reaction networks (CRNs) are a type of model commonly used in biology and chemistry. Their applications include the investigation of cellular system functions (systems biology), designing drugs (pharmacology), and forecasting epidemic progression (epidemiology). In this article, we present the Catalyst.jl software for the modelling, simulation, and analysis of CRNs across several physical scales. Catalyst simulations of CRN models are often one to two orders of magnitude faster than other popular CRN modeling tools. Such speed increases in turn aid in facilitating a variety of CRN analyses, for example simulating a model across a large number of conditions to check which ones best fit real-world observations. Catalyst also includes a domain-specific modeling language, which allows users to easily input their CRN models using standard chemical reaction syntax, thereby simplifying model creation. Finally, Catalyst is built on top of a widely used symbolic computer algebra system and mathematical modeling framework. This allows significant flexibility in the types of components that can be used within Catalyst CRN models, has enabled the development of tools to analyze and transform Catalyst models, and has helped Catalyst to become a broadly extensible package that can be composed with a variety of independent software libraries.