Additional Utilities for Tellurium that we have found useful in our work

Updated to 2.9. New version adds 'ei*(' terms to mass actions rate laws, eg

S1 -> S2; e1*(k1*S1 - k2*S2)

This makes it easier to compute control coefficients with repect to 'e'

Also added a new mass-action rate of the form:

v = k1*A(1 - (B/A)/Keq1)

These can be generated using the call:

model = teUtils.buildNetworks.getLinearChain(10, rateLawType="ModifiedMassAction")

Useful if you want to more easily control the equilbrium constant for a reaction.

This repo includes a number of useful utilities for Tellurium users. These include:

Installation

You can install teUtils using pip:

pip install teUtils

Documenation

The documentation can be found at: http://teUtils.readthedocs.io/en/latest/

buildNetworks

This modules provides two methods to build a linear chain of reactions using either mass-action or Michaelis-Menten kinetics or a random network using uniuni, unibi, biuni or bibi mass-action governed reactions.

odePrint

This provides a number of methods to convert SBML into the equations representing the model.

plotting

This modules contains a variety of additional plotting methods, include 3D, heatmaps for control coefficients, ascii plots, phase plots and more.

prettyTabular

This modules provides two methods to display fluxes and concentrations in a neat tabular format using jsut ascii characters.

fileUtils

File utilties that simply some operation whch for some reason are not available in Python

parameterScanning

This package only has one method currently which is a single method to make time course parameter scanning easier