synbiopython.genbabel.sedmlomexgen

Synbiopython (c) Global BioFoundry Alliance 2020

Synbiopython is licensed under the MIT License.

This module is to generate SEDML and COMBINE OMEX files.

class synbiopython.genbabel.sedmlomexgen.SEDMLOMEXgen.SEDMLOMEXgen

Bases: object

Class to generate the SEDML and COMBINE OMEX files.

static execute_inlineomex(inline_omex)

Execute the inline omex and generate the simulation figures.

export_omex(antimony_str, phrasedml_str, **kwargs)

Generate COMBINE OMEX file.

Parameters

• antimony_str (str) – represent the SBML

• phrasedml_str (str) – represent the SEDML

Returns

omex inline

Return type

str

Keyword Arguments

• outputfile: specify outputfile

static find_between(s, first, last)

Get the substring from string based on indexes.

Parameters

• s (str) – string to be searched

• first (str) – part of the string at the front

• last (str) – part of the string at the end

static get_omexfilename()

Return filename to the OMEX file according to the export time.

static get_sbml_biomodel(Biomodels_ID, **kwargs)

Get SBML model from biomodel. Use outputfile keyword argument to export the SBML model into .xml file at the specific path. A default .xml file will be generated by default at the temp directory.

Parameters

Biomodels_ID (str) – the ID for the Biomodels

Returns

the sbml in string format

Return type

str

Keyword Arguments

• outputfile: specify outputfile

phrasedmltosedml(phrasedml_str, sbml_file, **kwargs)

Generate SEDML file from phrasedml. Example of phrasedml_str: phrasedml_str = ‘’’ model1 = model “{}” … … ‘’’

Parameters

• phrasedml_str (str) – text-based way to represent SEDML

• sbml_file (str) – the SBML xml file/path to the file

Returns

the sedml string

Return type

str

static sbmltoantimony(sbmlfile)

Get the sbml file and return the antimony string.