PyscesToolbox 1.1.0

A set of metabolic model analysis tools for PySCeS.

PySCeSToolbox

This is a set of metabolic model analysis tools for PySCeS.

PySCeSToolbox currently provides tools for:

• Generalised supply-demand analysis.

• Symbolic metabolic control analysis and control pattern analysis.

• Generating model schemas from metabolic models.

• Distinguishing between thermodynamic and kinetic contributions towards reaction rate.

• Interactive plotting

PySCeSToolbox was designed to be used within the Jupyter notebook, but most of the core features should work in a normal Python script.

Documentation can be found at http://pyscestoolbox.readthedocs.io. While all major tools have been documented, the documentation is still a work in progress. A PDF copy of the documentation is also included in the site-packages/psctb/docs subfolder of the Python prefix where PySCeSToolbox is installed.

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

For readers of “Tracing regulatory routes in metabolism using generalised supply-demand analysis” published in BMC Systems Biology

To use the Jupyter notebook file included as “Additional file 5” in the paper, please install the latest version of PySCeSToolbox specified under Installation.

The two PySCeS MDL model files included as “Additional file 1” and “Additional file 2” are required to run the notebook. They should be renamed to “Hoefnagel_moiety_ratio.psc” and “Curien.psc”, respectively. Further instructions are included within the notebook and on this page.

Changes:

Because this project is undergoing development, future changes might break older scripts. These types of changes will be kept to a minimum and will be documented here.

Changes on 2017-02-09: Full cross compatibility

On 2017-02-09 Symca support via Maxima has been added to PySCeSToolbox on Windows. A configuration file located at C:\Pysces\psctb_config.ini can be used to specify the path to maxima.bat. By default, however, PySCeSToolbox should detect the path to maxima.bat automatically if it has been installed using the default options. This change should have no impact on any older scripts save for making them platform independent.

Changes on 2017-02-02: Dropped IPython Notebook 3.x.x support

As of 2017-02-02 IPython Notebook 3.x.x support has been dropped in favour of Jupyter 4.x.x. This should not affect the functioning of scripts (save for those based on versions before that of 2015-11-11). PySCeSToolbox will however require the Jupyter Notebook as of this date in order to use its interactive features. Note that ipywidgets (an automatically installed requirement for the Jupyter notebook) needs you to run the command “jupyter nbextension enable --py --sys-prefix widgetsnbextension” before enabling widgets in the notebook.

Changes on 2015-11-11: API changes

Major changes were made on 2015-11-11 that might break scripts coded before this date. These changes are related to the naming of methods and fields. For scripts older than 2015-11-11 we recommend using an older version of PySCeSToolbox (noted under Installation). Manual porting of scripts is also possible with details of necessary changes outlined under Porting scripts to latest version.

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

Old name	New Name
save	save_session
load	load_session
plot_data	scan_results
mca_data	mca_results
plot_decompose	do_mca_scan

Thermokin

Old name	New Name
reactions	reaction_results
mca_data	ec_results
reaction name*	J_reaction name
par_scan	do_par_scan

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

Symca

Old name	New Name
CC	cc_results
CCn*	cc_results_n
save	save_session
load	load_session
par_scan	do_par_scan

*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

Old name	New Name
plot_data	scan_results
save_data	save_results