Help on module cameo.flux_analysis.analysis in cameo.flux_analysis:
NAME
cameo.flux_analysis.analysis
FILE
/Users/joao/Documents/repos/cameo/cameo/flux_analysis/analysis.py
DESCRIPTION
# Copyright 2014 Novo Nordisk Foundation Center for Biosustainability, DTU.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
FUNCTIONS
fbid(model, knockouts, view=<cameo.parallel.SequentialView object>, method='fva')
Flux balance impact degree by Zhao et al 2013
:param model: wild-type model
:param knockouts: list of reaction knockouts
:param method: the method to compute the perturbation. default is "fva" - Flux Variability Analysis.
It can also be computed with "em" - Elementary modes
:return: perturbation
flux_variability_analysis(model, reactions=None, fraction_of_optimum=0.0, remove_cycles=True, view=None)
Flux variability analysis.
Parameters
----------
model: SolverBasedModel
reactions: None or iterable
The list of reaction whose lower and upper bounds should be determined.
If `None`, all reactions in `model` will be assessed.
view: SequentialView or MultiprocessingView or ipython.cluster.DirectView
A parallelization view.
Returns
-------
pandas.DataFrame
Pandas DataFrame containing the results of the flux variability analysis.
phenotypic_phase_plane(model, variables=[], objective=None, points=20, view=None)
Phenotypic phase plane analysis.
Parameters
----------
model: SolverBasedModel
variables: str or reaction or iterable
A reaction ID, reaction, or list of reactions to be varied.
objective: str or reaction or optlang.Objective
An objective to be minimized/maximized for
points: int or iterable
Number of points to be interspersed between the variable bounds.
A list of same same dimensions as `variables` can be used to specify
variable specific numbers of points.
view: SequentialView or MultiprocessingView or ipython.cluster.DirectView
A parallelization view.
Returns
-------
PhenotypicPhasePlaneResult
The phenotypic phase plane.
DATA
__all__ = ['flux_variability_analysis', 'phenotypic_phase_plane', 'fbi...