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Catalyst.jl is a symbolic modeling package for analysis and high-performance simulation of chemical reaction networks. Catalyst defines symbolic ReactionSystems, which can be created programmatically or easily specified using Catalyst's domain-specific language (DSL). Leveraging ModelingToolkit and Symbolics.jl, Catalyst enables large-scale simulations through auto-vectorization and parallelism. Symbolic ReactionSystems can be used to generate ModelingToolkit-based models, allowing the easy simulation and parameter estimation of mass action ODE models, Chemical Langevin SDE models, stochastic chemical kinetics jump process models, and more. Generated models can be used with solvers throughout the broader SciML ecosystem, including higher-level SciML packages (e.g. for sensitivity analysis, parameter estimation, machine learning applications, etc).
Features
- Tutorials and documentation
- A DSL provides a simple and readable format for manually specifying chemical reactions
- Graphviz can be used to generate and visualize reaction network graphs
- Non-integer (e.g. Float64) stoichiometric coefficients are supported for generating ODE models, and symbolic expressions for stoichiometric coefficients are supported for all system types
- Catalyst ReactionSystems provide a symbolic representation of reaction networks, built on ModelingToolkit.jl and Symbolics.jl
- Coupled differential and algebraic constraint equations can be included in Catalyst models, and are incorporated during conversion to ODEs or steady state equations
Project Samples
