# Catalyst.jl for Reaction Models

Catalyst.jl is a symbolic modeling package for analysis and high performance simulation of chemical reaction networks. Catalyst defines symbolic `ReactionSystem`

s, 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 `ReactionSystem`

s 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

- DSL provides a simple and readable format for manually specifying chemical reactions.
- Catalyst
`ReactionSystem`

s provide a symbolic representation of reaction networks, built on ModelingToolkit.jl and Symbolics.jl. - The Catalyst.jl API provides functionality for extending networks, building networks programmatically, network analysis, and for composing multiple networks together.
`ReactionSystem`

s generated by the DSL can be converted to a variety of`ModelingToolkit.AbstractSystem`

s, including symbolic ODE, SDE and jump process representations.- By leveraging ModelingToolkit, users have a variety of options for generating optimized system representations to use in solvers. These include construction of dense or sparse Jacobians, multithreading or parallelization of generated derivative functions, automatic classification of reactions into optimized jump types for Gillespie type simulations, automatic construction of dependency graphs for jump systems, and more.
- Generated systems can be solved using any DifferentialEquations.jl ODE/SDE/jump solver, and can be used within
`EnsembleProblem`

s for carrying out parallelized parameter sweeps and statistical sampling. Plot recipes are available for visualizing the solutions. - Julia
`Expr`

s can be obtained for all rate laws and functions determining the deterministic and stochastic terms within resulting ODE, SDE or jump models. - Latexify can be used to generate LaTeX expressions corresponding to generated mathematical models or the underlying set of reactions.
- Graphviz can be used to generate and visualize reaction network graphs. (Reusing the Graphviz interface created in Catlab.jl.)
- Catalyst
`ReactionSystem`

s can be imported from SBML files via SBMLToolkit.jl, and from BioNetGen .net files and various matrix network representations using ReactionNetworkImporters.jl.

## Installation

Catalyst can be installed through the Julia package manager:

```
]add Catalyst
using Catalyst
```

## Illustrative Example

Here is a simple example of generating, visualizing and solving an SIR ODE model. We first define the SIR reaction model using Catalyst

```
using Catalyst
rn = @reaction_network begin
α, S + I --> 2I
β, I --> R
end α β
```

Assuming Graphviz and is installed and *command line accessible*, the network can be visualized using the `Graph`

command

`Graph(rn)`

which in Jupyter notebooks will give the figure

To generate and solve a mass action ODE version of the model we use

```
using DiffEqBase, OrdinaryDiffEq
p = [.1/1000, .01] # [α,β]
tspan = (0.0,250.0)
u0 = [999.0,1.0,0.0] # [S,I,R] at t=0
op = ODEProblem(rn, species(rn) .=> u0, tspan, parameters(rn) .=> p)
sol = solve(op, Tsit5()) # use Tsit5 ODE solver
```

which we can plot as

```
using Plots
plot(sol, lw=2)
```

## Getting Help

Catalyst developers are active on the Julia Discourse, and the Julia Slack channels #sciml-bridged and #sciml-sysbio. For bugs or feature requests open an issue.