HetaImporter.jl

HetaImporter.jl is a Julia package for importing Heta models into Julia. Internally HetaImporter uses Heta-compiler, a CLI tool that converts Systems Biology/QSP models written in the Heta modeling language into various formats suiatble for simulation, calibration, and analysis (e.g., SBML, SimBiology, mrgsolve, and Julia code).

The package supports two ways for converting Heta models into Julia code:

• ir_format = :julia: call heta-compiler's Julia exporter to generate Julia source file model.jl.
• ir_format = :dynms: call heta-compiler's DynMS exporter, parse output.dynms.json, and generate readable Julia source from the DynMS intermediate representation.

The generated Julia file is intended to be loaded by simulation and parameters estimation packages such as HetaSimulator.

Quick Start

using HetaImporter

julia_path = build_julia_file(
  "path/to/heta/platform";
  ir_format = :dynms,
  build_dir = "path/to/build"
)

The returned julia_path points to:

joinpath(build_dir, HetaImporter.JULIA_MODEL_DIR, HetaImporter.JULIA_MODEL_NAME)

To use heta-compiler's Julia exporter directly:

julia_path = build_julia_file(
  "path/to/heta/platform";
  ir_format = :julia,
  build_dir = "path/to/build"
)

DynMS Parser

DynMS JSON can also be parsed directly:

dynms_path = build_dynms_file(
  "path/to/heta/platform";
  build_dir = "path/to/build"
)

spec = parse_dynms_spec(dynms_path)
model = spec.models[:my_model]

The parsed DynMSSpec is a representation of the DynMS content (states, assignment rules, events, etc) in the form of Julia expressions Expr.

Pages

• API