8.1.1.1.1.3. skimpy.analysis.modal

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Copyright 2018 Laboratory of Computational Systems Biotechnology (LCSB), Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland

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

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8.1.1.1.1.3.1. Submodules

8.1.1.1.1.3.2. Package Contents

8.1.1.1.1.3.2.1. Classes

TabDict

Really just an ordered dict with tab completion in interactive terminals

FluxFunction

8.1.1.1.1.3.2.2. Functions

modal_matrix

class skimpy.TabDict

Bases: collections.OrderedDict

Really just an ordered dict with tab completion in interactive terminals

__dir__(self)

__dir__() -> list default dir() implementation

__getattr__(self, attr)
iloc(self, ix)
class skimpy.FluxFunction(variables, expr, parameters, pool=None)
__call__(self, concentrations, parameters)
skimpy.modal_matrix(kmodel, concentration_dict, parameters, flux_modes=False, tolerance=1e-12)

This function computes the transformation matrix W as described in Chapter 4 of Heinrich, Reinhart, and Stefan Schuster. The regulation of cellular systems. Springer Science & Business Media, 2012.

The matrix W describes the composition of each pool variable X[i] whos dynamics are given by the eigenvalue lam[i] as a linear combination of the model variables S, which are concentrations.

Parameters

  • kmodel – A skimpy.core.KineticModel with compiled mca functions

  • concentration_dict – A dict {‘variable_name’: value, }

  • parameters – A dict {‘param_name’: value, }

Returns