  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.
