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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.