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 is a domain-specific language (DSL) for high-performance simulation and modeling of chemical reaction networks. Catalyst utilizes ModelingToolkit
ReactionSystems, leveraging ModelingToolkit to enable large-scale simulations through auto-vectorization and parallelism.
ReactionSystems can be used to generate ModelingToolkit-based models, allowing 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.).
ReactionSystems generated by the DSL can be converted to a variety of
ModelingToolkit.AbstractSystems, including ODE, SDE, and jump process representations.
EnsembleProblems for carrying out GPU-parallelized parameter sweeps and statistical sampling. Plot recipes are available for visualizing the solutions.
Exprs can be obtained for all rate laws and functions determining the deterministic and stochastic terms within resulting ODE, SDE, or jump models.
rs = @reaction_network begin c1, S + E --> SE c2, SE --> S + E c3, SE --> P + E end c1 c2 c3 p = (0.00166,0.0001,0.1) # [c1,c2,c3] tspan = (0., 100.) u0 = [301., 100., 0., 0.] # [S,E,SE,P]
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")
using Catalyst, Plots, StochasticDiffEq, DiffEqJump rs = @reaction_network begin c1, X --> 2X c2, X --> 0 c3, 0 --> X end c1 c2 c3 p = (1.0,2.0,50.) # [c1,c2,c3] tspan = (0.,10.) u0 = [5.] # [X] sprob = SDEProblem(rs, u0, tspan, p) ssol = solve(sprob, LambaEM(), reltol=1e-3) plot(ssol,lw=2,title="Adaptive SDE: Birth-Death Process")