memote.support.matrix

Supporting functions checking the matrix condition of the model object.

Module Contents

Functions

absolute_extreme_coefficient_ratio(model)	Return the maximum and minimum absolute, non-zero coefficients.
number_independent_conservation_relations(model)	Return the number of conserved metabolite pools.
matrix_rank(model)	Return the rank of the model’s stoichiometric matrix.
degrees_of_freedom(model)	Return the degrees of freedom, i.e., number of “free variables”.

memote.support.matrix.LOGGER

memote.support.matrix.absolute_extreme_coefficient_ratio(model)

Return the maximum and minimum absolute, non-zero coefficients.

Parameters:

model : cobra.Model

The metabolic model under investigation.

memote.support.matrix.number_independent_conservation_relations(model)

Return the number of conserved metabolite pools.

This number is given by the left null space of the stoichiometric matrix.

Parameters:

model : cobra.Model

The metabolic model under investigation.

memote.support.matrix.matrix_rank(model)

Return the rank of the model’s stoichiometric matrix.

Parameters:

model : cobra.Model

The metabolic model under investigation.

memote.support.matrix.degrees_of_freedom(model)

Return the degrees of freedom, i.e., number of “free variables”.

Parameters:

model : cobra.Model

The metabolic model under investigation.

Notes

This specifically refers to the dimensionality of the (right) null space of the stoichiometric matrix, as dim(Null(S)) corresponds directly to the number of free variables in the system [1]. The formula used calculates this using the rank-nullity theorem [2].

References

[1]	Fukuda, K. & Terlaky, T. Criss-cross methods: A fresh view on pivot algorithms. Mathematical Programming 79, 369-395 (1997).

[2]	Alama, J. The Rank+Nullity Theorem. Formalized Mathematics 15, (2007).