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Model Libraries and Importers

Models are passed on from generation to generation. Many models are not built from scratch but have a legacy of the known physics, biology, and chemistry embedded into them. Julia's SciML offers a range of pre-built modeling tools, from reusable acausal components to direct imports from common file formats.

ModelingToolkitStandardLibrary.jl: A Standard Library for ModelingToolkit

Given the composable nature of acausal modeling systems, it's helpful to not have to define every component from scratch and instead build off a common base of standard components. ModelingToolkitStandardLibrary.jl is that library. It provides components for standard models to start building everything from circuits and engines to robots.

DiffEqCallbacks.jl: Pre-Made Callbacks for DifferentialEquations.jl

DiffEqCallbacks.jl has many event handling and callback definitions which allow for quickly building up complex differential equation models. It includes:

  • Callbacks for specialized output and saving procedures
  • Callbacks for enforcing domain constraints, positivity, and manifolds
  • Timed callbacks for periodic dosing, presetting of tstops, and more
  • Callbacks for determining and terminating at steady state
  • Callbacks for controlling stepsizes and enforcing CFL conditions
  • Callbacks for quantifying uncertainty with respect to numerical errors

SBMLToolkit.jl: SBML Import

SBMLToolkit.jl is a library for reading SBML files into the standard formats for Catalyst.jl and ModelingToolkit.jl. There are well over one thousand biological models available in the BioModels Repository.

CellMLToolkit.jl: CellML Import

CellMLToolkit.jl is a library for reading CellML files into the standard formats for ModelingToolkit.jl. There are several hundred biological models available in the CellML Model Repository.

ReactionNetworkImporters.jl: BioNetGen Import

ReactionNetworkImporters.jl is a library for reading BioNetGen .net files and various stoichiometry matrix representations into the standard formats for Catalyst.jl and ModelingToolkit.jl.

ModelingToolkitNeuralNets.jl: Neural Network Blocks in Acausal Models

ModelingToolkitNeuralNets.jl provides neural-network components in the style of ModelingToolkitStandardLibrary, so a universal differential equation can be wired into part of an ODESystem through RealInputArray / RealOutputArray connectors.

BaseModelica.jl: Base Modelica Import

BaseModelica.jl parses Base Modelica models into Julia objects and converts them to ModelingToolkit systems.

DiffEqPhysics.jl: Hamiltonian and Physics-Based Problem Constructors

DiffEqPhysics.jl builds differential-equation problems from physical descriptions such as Hamiltonians, for use with the DiffEq solvers.

DiffEqFinancial.jl: Financial Models

The goal of DiffEqFinancial.jl is to be a feature-complete set of models for the types of problems found in libraries like QuantLib, such as the Heston process or the Black-Scholes model.

PubChem.jl and PubChemReactions.jl: Chemical Data Import

PubChem.jl attaches PubChem metadata to Catalyst species. PubChemReactions.jl generates reaction networks from PubChem data.

Pyomo.jl: Pyomo via Symbolics.jl

Pyomo.jl is a Julia interface to Pyomo that builds expressions through Symbolics.jl, so nonlinear optimization and DAE models defined in Pyomo can interoperate with the Julia symbolic stack.

MathML.jl: MathML Parser

MathML.jl parses MathML into Symbolics.jl expressions.

CasADi.jl: CasADi Interface

CasADi.jl is a Julia interface to CasADi via PythonCall.