juliaepi/catalyst.jl

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software

Catalyst.jl

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).

Breaking Changes and New Features

Breaking changes and new functionality are summarized in the HISTORY.md file.

Tutorials and Documentation

For tutorials and information on using the package, see the stable documentation. The in-development documentation describes unreleased features in the current master branch.

Several Youtube video tutorials and overviews are also available:

• From JuliaCon 2022: A three hour tutorial workshop overviewing how to use Catalyst and its more advanced features as of version 12.1. Workshop video, Workshop Pluto.jl Notebooks.
• From SIAM CSE 2021: A short 15 minute overview of Catalyst as of version 6 is available in the talk Modeling Biochemical Systems with Catalyst.jl.
• From JuliaCon 2018: A short 13 minute overview of Catalyst when it was known as DiffEqBiological in older versions is available in the talk Efficient Modelling of Biochemical Reaction Networks

Features

• DSL provides a simple and readable format for manually specifying chemical reactions.
• Catalyst ReactionSystems provide a symbolic representation of reaction networks, built on ModelingToolkit.jl and Symbolics.jl.
• 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.
• The Catalyst.jl API provides functionality for extending networks, building networks programmatically, network analysis, and for composing multiple networks together.
• ReactionSystems generated by the DSL can be converted to a variety of ModelingToolkit.AbstractSystems, including symbolic ODE, SDE, and jump process representations.
• Conservation laws can be detected and applied to reduce system sizes, and generate non-singular Jacobians, during conversion to ODEs, SDEs, and steady-state equations.
• 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 EnsembleProblems for carrying out parallelized parameter sweeps and statistical sampling. Plot recipes are available for visualizing the solutions.
• Symbolics.jl symbolic expressions and Julia Exprs 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.)

Packages Supporting Catalyst

• Catalyst ReactionSystems can be imported from SBML files via SBMLToolkit.jl, and from BioNetGen .net files and various stoichiometric matrix network representations using ReactionNetworkImporters.jl.
• MomentClosure.jl allows generation of symbolic ModelingToolkit ODESystems, representing moment closure approximations to moments of the Chemical Master Equation, from reaction networks defined in Catalyst.
• FiniteStateProjection.jl allows the construction and numerical solution of Chemical Master Equation models from reaction networks defined in Catalyst.
• DelaySSAToolkit.jl can augment Catalyst reaction network models with delays, and can simulate the resulting stochastic chemical kinetics with delays models.

Illustrative Examples

Gillespie Simulations of Michaelis-Menten Enzyme Kinetics

using Catalyst, Plots, JumpProcesses
rs = @reaction_network begin
  c1, S + E --> SE
  c2, SE --> S + E
  c3, SE --> P + E
end c1 c2 c3
p     = (:c1 => 0.00166, :c2 => 0.0001, :c3 => 0.1)
tspan = (0., 100.)
u0    = [:S => 301, :E => 100, :SE => 0, :P => 0]

# solve JumpProblem
dprob = DiscreteProblem(rs, u0, tspan, p)
jprob = JumpProblem(rs, dprob, Direct())
jsol = solve(jprob, SSAStepper())
plot(jsol,lw=2,title="Gillespie: Michaelis-Menten Enzyme Kinetics")

Adaptive SDEs for A Birth-Death Process

using Catalyst, Plots, StochasticDiffEq
rs = @reaction_network begin
  c1, X --> 2X
  c2, X --> 0
  c3, 0 --> X
end c1 c2 c3
p     = (:c1 => 1.0, :c2 => 2.0, :c3 => 50.)
tspan = (0.,10.)
u0    = [:X => 5.]
sprob = SDEProblem(rs, u0, tspan, p)
ssol  = solve(sprob, LambaEM(), reltol=1e-3)
plot(ssol,lw=2,title="Adaptive SDE: Birth-Death Process")

Getting Help

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