Documentation for teUtils Version 0.99

This page describes the teUtils package.

Installation

To install teUtils use

pip install teUtils

For additional information go to https://github.com/sys-bio/teUtils

To read more about Tellurium, go to http://tellurium.analogmachine.org/

Overview

teUtils is a utilties package for Telluirum that provides a number of useful function. These are grouped into:

• Plotting

• Random Network Construction

• Parameter Scanning

• Pretty Tabular Output

• Converting SBML in to Readable Differential Equations

• File Utilties

Examples

import teUtils as tu
# Build a random network using mass-action kintics with upto 10 species and 20 reactions
antimonyModel = tu.buildNetworks.getRandomNetwork(10, 20)

# Plot the species cocnentrations as a histogram for the roadrunne rmodel r
tu.plotting.plotFloatingSpecies(r)

# Plot a heatmap of the flux control coefficients
tu.plotting.plotFluxControlHeatMap (r)

# Plot a grid of phase portraits of all species in the model r
tu.plotting.plotFluxControlHeatMap (r)

# Generate the ODES for a SBML model stored in a file
tu.odePrint.getODEsFromSBMLFile ('mymodel.xml')

Contents:

• Random Network Building Utilities
  • Settings
  • getLinearChain()
  • getRandomNetworkDataStructure()
  • getRandomNetwork()
• Plotting Utilities
  • plotAsciiConcentrationsBar()
  • plotAsciiReactionRatesBar()
  • plotRandSimGrid()
  • plotPhasePortraitGrid()
  • plotConcentrationControlHeatMap()
  • plotFluxControlHeatMap()
  • plotFluxControlBar()
  • plotConcentrationControlBar()
  • plotArrayHeatMap()
  • plotConcentrationControlIn3D()
  • plotFluxControlIn3D()
  • plotReactionRates()
  • plotFloatingSpecies()
  • plotArray()
  • testme()
• Simple Parmameter Scanning Functions
  • simpleTimeCourseScan()
• ODE Printing Utilities
  • getODEsFromSBMLFile()
  • getODEsFromSBMLString()
  • getODEsFromModel()
• Generate Simple Tabular Data
  • tabulateConcentrations()
  • tabulateFluxes()
• File Utilities
  • readCsvFile()