Metabolitics¶

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Installation¶

You can install metabolitics with pip:

pip install metabolitics

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For more features, You can check the documentation.

The documentation of the project avaiable in http://metabolitics.rtfd.io .

class metabolitics.analysis.MetaboliticsAnalysis(model, without_transports=True, timeout=600)[source]¶

Metabolitics analysis for metabolic dataset.

__init__(model, without_transports=True, timeout=600)[source]¶

Parameters:	model – cobra Model

add_constraint(measured_metabolites)[source]¶

Add measurements as constraint to model.

Parameters:	measured_metabolites (dict) – dict in which keys are metabolite names and values are float numbers represent fold changes in metabolites.

set_objective(measured_metabolites)[source]¶

Updates objective function for given measured metabolites.

Parameters:	measured_metabolites (dict) – dict in which keys are metabolite names and values are float numbers represent fold changes in metabolites.

metabolitics.utils.load_network_model(model)[source]¶

Loads metabolic network models in metabolitics.

Parameters:	model (str) – model name

metabolitics.utils.load_metabolite_mapping(naming_file='pubChem')[source]¶

Loads metabolite name mapping from different databases to recon.

Parameters:	naming_file (str) – names of databases

valid options {‘kegg’, ‘pubChem’, ‘cheBl’, ‘hmdb’, ‘toy’}

This packages includes extension methods for cobra models.

metabolitics.extensions.is_transport_subsystem¶

staticmethod(function) -> method

Convert a function to be a static method.

A static method does not receive an implicit first argument. To declare a static method, use this idiom:

class C:

@staticmethod def f(arg1, arg2, …):

…

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class.

Static methods in Python are similar to those found in Java or C++. For a more advanced concept, see the classmethod builtin.