CellCollective

class cellcollective.CellCollectiveConnector(identifier, version=1)

property sbml_basename

property sbml_urls

class cellcollective.CellCollectiveSBMLModel(localfile)

property species

Returns the set of defined species

Return type:

set

species_metadata(name)

species_ncbi_gene(name)

species_uniprotkb(name)

cellcollective.connect(identifier)

cellcollective.id_from_url(url)

cellcollective.load(identifier, auto_persistent=True)

Load a CellCollective model from its URL or SBML export.

identifier can be: - a URL of the form "cellcollective://{model_id}:{model_version}" - the model URL from research.cellcollective.org - the location of the SBML file exported from CellCollective

Whenever identifier is one of the two first cases, the module relies on the online API of CellCollective to download the SBML file. As the API may change over time, it is strongly recommended to rely on instead on downloaded SBML files and attach them with the notebook to ensure its repeatibility over time.

With the option auto_persistent=True, the module first looks for an existing downloaded SBML file. If it does not exists, it uses the online API to download it and move it alongside the notebook.

cellcollective.to_biolqm(model)

cellcollective.url_matches(url)