Computing the Frequency Response of Biochemical Networks: A Python module

TL;DR

This paper introduces a Python software package that computes the frequency response of biochemical networks, accommodating conserved moieties and providing tools for visualization, with applications demonstrated on reaction chains and feedback systems.

Contribution

The paper presents a novel Python module capable of analyzing the frequency response of biochemical networks from standard models, including conserved moieties and phase discontinuities.

Findings

Effective computation of frequency response for biochemical networks.

Demonstrated analysis of reaction chains and feedback effects.

Software available as open source for broad use.

Abstract

In this paper, a set of Python methods is described that can be used to compute the frequency response of an arbitrary biochemical network given any input and output. Models can be provided in standard SBML or Antimony format. The code takes into account any conserved moieties so that this software can be used to also study signaling networks where moiety cycles are common. A utility method is also provided to make it easy to plot standard Bode plots from the generated results. The code also takes into account the possibility that the phase shift could exceed 180 degrees which can result in ugly discontinuities in the Bode plot. In the paper, some of the theory behind the method is provided as well as some commentary on the code and several illustrative examples to show the code in operation. Illustrative examples include linear reaction chains of varying lengths and the effect of negative feedback on the frequency response. Software License: MIT Open Source Availability: The code is available from https://github.com/sys-bio/frequencyResponse.