IntroductionΒΆ

PySCeSToolbox is a set of extensions to the original Python Simulator for Cellular Systems (PySCeS) [1]. The goals of this software are (1) to provide metabolic model analysis tools that are beyond the scope of PySCeS and (2) to provide a streamlined framework for using these tools together. The reader is referred to the Bioinformatics paper [2] for further details.

Currently, PySCeSToolbox includes three main analysis tools:

  1. SymCa for performing symbolic control analysis [3,4].

  2. RateChar for performing generalised supply demand analysis [5,6].

  3. ThermoKin for distinguishing between the thermodynamic and kinetic contributions towards reaction rates and enzyme elasticities [7,8].

In addition to these tools PySCeSToolbox provides functionality for displaying interactive plots, tables of results, and typeset mathematical expressions and symbols by making extensive use of the wonderful Jupyter (IPython) Notebook platform. Therefore, in order to make the best use of its features we recommend that users run PySCeSToolbox within the IPython Notebook environment. Regardless of being designed for interactive work through the Notebook, the core features are completely compatible with traditional python scripting.

We recommend that users unfamiliar with PySCeS refer to its documentation before continuing here.