odefac¶

Convert SBML models to ODE systems for various programming languages.

This allows easy integration with existing workflows by rendering respective code templates.

Currently supported code generation: - python: scipy - R: desolve - R: dmod

The following SBML core constructs are currently NOT supported: - ConversionFactors - FunctionDefinitions - InitialAssignments - Events - Piecewise functions - Dynamical changing compartments - Species with AssignmentRules

SBML2ODE ¶

SBML2ODE(doc)

SBML to ODE converter.

Writes out python or R ODE files which can be solved with standard integrators like scipy odeint or R desolve.

Init with SBMLDocument.

:param doc: SBMLDocument

info ¶

info()

Print information on ODE system to console.

from_file `classmethod` ¶

from_file(sbml_file)

Create converter from SBML file.

dependency_graph `staticmethod` ¶

dependency_graph(y, filtered_ids)

Create dependency graph from given dictionary.

:param y: { variable: astnode } dictionary :param filtered_ids: ids which are defined elsewhere and not part of dependency tree :return:

to_python ¶

to_python(py_file=None)

Write ODEs to python.

to_tex ¶

to_tex(tex_file=None)

Write ODEs to tex/latex.

to_R ¶

to_R(r_file=None)

Write ODEs to R.

to_julia ¶

to_julia(jl_file=None)

Write ODEs to julia.

Generated files can be used as an input for DifferentialEquations.jl https://docs.sciml.ai/DiffEqDocs/stable/

to_markdown ¶

to_markdown(md_file=None)

Write ODEs to markdown.

to_custom_template ¶

to_custom_template(template_file, output_file=None)

Write ODEs to custom template.