cobra.io.web.load#

Provide a function load_model to access remote model repositories.

Attributes#

`logger`
`configuration`
`DEFAULT_REPOSITORIES`

Functions#

`load_model`(→ cobra.core.Model)	Download an SBML model from a remote repository.
`_fetch_model`(→ bytes)	Attempt to load a gzip-compressed SBML document from the given repositories.
`get_model_from_gzip_sbml`(→ cobra.core.Model)	Generate a model instance from a gzip-compressed, UTF-8 encoded SBML document.

Module Contents#

cobra.io.web.load.logger#

cobra.io.web.load.configuration#

cobra.io.web.load.DEFAULT_REPOSITORIES#

cobra.io.web.load.load_model(model_id: str, repositories: Iterable[cobra.io.web.abstract_model_repository.AbstractModelRepository] = DEFAULT_REPOSITORIES, cache: bool = True) → cobra.core.Model[source]#

Download an SBML model from a remote repository.

Downloaded SBML documents are by default stored in a cache on disk such that future access is much faster. By default, models can be loaded from the following repositories:

BiGG Models
BioModels

You can use the AbstractModelRepository class as a parent to implement your own repository accessor which you pass to the load_model function. In case you implement a new interface, please consider submitting a pull request to COBRApy.

Parameters:

model_id (str) – The identifier of the desired metabolic model. This is typically repository specific.
repositories (iterable, optional) – An iterable of repository accessor instances. The model_id is searched in order.

Returns:

A model instance generated from the SBML document.

Return type:

Model

Raises:

RuntimeError – As with any internet connection, there are multiple errors that can occur.

Examples

# Most of the time calling load_model with an identifier should be enough. >>> print(load_model(“e_coli_core”)) e_coli_core >>> print(load_model(“MODEL1510010000”)) MODEL1510010000