PyscesToolbox 1.0.0

Contents of README

• Requirements

• Installation

• Basic usage

• Important notices

• Porting scripts to latest version

Requirements

An abbreviated list of requirements is given below. Python dependencies will be installed automatically when installing PySCeSToolbox via pip or with conda. For detailed operating system-specific instructions on installing the requirements see the documentation at http://pyscestoolbox.readthedocs.io/.

• A Python 3.x installation (versions 3.6-3.8 recommended)

• The full SciPy stack (see http://scipy.org/install.html)

• PySCeS (see http://pysces.sourceforge.net/download.html)

• Maxima (see http://maxima.sourceforge.net/download.html)

• Jupyter Notebook (jupyter-core version in the 4.x.x series)

Notes:

Required packages should automatically download and install when using the commands specified under Installation below.

Maxima is only a requirement for SymCA.

Installation

Note: Detailed installation instructions are provided here.

The latest release of PySCeSToolbox can be installed either on Anaconda or from PyPI by running the following commands in the terminal (or Windows equivalent).

Install on Anaconda:

conda install -c pysces -c sbmlteam pyscestoolbox

Install from PyPi using pip:

pip install pyscestoolbox

To enable widgets you may need to run the following commands:

jupyter nbextension enable --py --sys-prefix widgetsnbextension
jupyter nbextension install --py --user d3networkx_psctb
jupyter nbextension enable --py --user d3networkx_psctb

The latest development version can be installed from GitHub with:

pip install git+https://github.com/PySCeS/PySCeSToolbox.git

For the pre-2015-11-11 version:

pip install git+https://github.com/exe0cdc/ipython-d3networkx.git
pip install git+https://github.com/PySCeS/PySCeSToolbox.git@f63b5ab660f103105750159885608a5f48de1551

Basic usage

To start a PySCeSToolbox session in a Jupyter notebook:

1. Start up the Jupyter Notebook using the jupyter notebook command in the terminal

2. Create a new notebook by clicking the New button on the top right of the window and selecting Python 3

3. Run the following three commands in the first cell:

import pysces
import psctb
%matplotlib inline

Model files must be placed in ~/Pysces/psc/ if using Linux or macOS, and in C:\Pysces\psc\ for Windows (PySCeS version < 0.9.8) or C:\Users\<username>\Pysces\psc (PySCeS version 0.9.8+).

Important notices

Porting scripts to latest version

Method and variable names and the analysis objects they belong to that were changed on 2015-11-11 are documented in the tables below. To port any older script simply change the old name of any method/variable to the new name.

RateChar

Thermokin

*reaction name refers to the naming of a reaction as it is defined in the model file.

Symca

*CCn refers to any of the additional result dictionaries that are created when an internal metabolite is fixed and the internal_fixed paramenter of do_symca is set to True

Data2D