Installation

PySCeSToolbox is compatible with macOS, Linux, and Windows. Operating system-specific instructions are discussed in the sections below. We have made special effort to provide as detailed instructions as possible, assuming a clean installation of each operating system prior to installation of PySCeSToolbox, and relatively limited knowledge of Python. If further assistance is required, please contact the developers.

Abbreviated requirements

PySCeSToolbox has a number of requirements that must be met before installation can take place. Fortunately most requirements, save for a few exceptions (as discussed in the operating system-specific sections), will be taken care of automatically during installation. An abbreviated list of requirements follows:

Windows

Windows requires the manual installation of Python 3.x, PySCeS and Maxima. Installation was tested on Windows 10.

Python

For Windows users (especially those unfamiliar with Python) we recommend using the Anaconda Python distribution (https://www.anaconda.com/products/individual#Downloads). This is a low fuss solution that will install Python on you system together with many of the packages necessary for running PySCeSToolbox. Download the appropriate Python 3.7 package from the download page (most probably the 64bit edition) and follow the instructions of the installation wizard.

If you prefer more fine-grained control it is also possible to install Python from Python.org (https://www.python.org/downloads/windows/); be sure to install pip as well when prompted by the installer, and add the Python directories to the system PATH.

PySCeS

If you installed Anaconda, PySCeS can be installed by opening a command prompt in an Anaconda environment (Python 3.6 or 3.7) and executing the command:

conda install -c sbmlteam -c pysces pysces

If you installed Python from Python.org directly, open a Windows Command Prompt, verify that the Python paths are set up correctly by checking the pip version and install PySCeS by executing:

pip -V
pip install pysces

Currently Python versions 3.6-3.8 are supported with a pip install.

Maxima

Maxima is necessary for generating control coefficient expressions using SymCA. The latest version of Maxima can be downloaded and installed from the Windows download page at http://maxima.sourceforge.net/download.html.

Windows might also require the path to maxima.bat to be defined in the psctb_config.ini file, found at C:\Pysces\psctb_config.ini by default.

Note

As of PySCeS version 0.9.8 the default location of configuration and model files moved from C:\Pysces to %USERPROFILE%\Pysces, i.e. typically C:\Users\<username>\Pysces, to bring the Windows installation more in line with the macOS and Linux installations. Refer to the PySCeS 0.9.8 release notes for more information.

The default path included in psctb_config.ini is set as C:\maxima?\bin\maxima.bat, where the question marks are wildcards (since the specific path will depend on the version of Maxima). If Maxima has been installed to a user specified directory, the correct path to the maxima.bat file must be specified here.

PySCeSToolbox

Now you are ready to install PySCeSToolbox. If you are using Anaconda, open up the Anaconda Command Prompt (Start –> Anaconda Command Prompt), else open up the Windows Command Prompt if you installed PySCeS with pip. In the command prompt, type in and execute the command:

pip install pyscestoolbox

This will automatically download both PySCeSToolbox and any outstanding requirements.

Enabling widgets

If you are running the Jupyter notebook for the first time, or if you have not yet enabled the notebook widgets you may need to run the following command:

jupyter nbextension enable --py --sys-prefix widgetsnbextension

We also recommend running the following two commands to enable the ModelGraph functionality of PySCeSToolbox. Rerunning this command may be necessary when updating/reinstalling PySCeSToolbox.

jupyter nbextension install --py --user d3networkx_psctb
jupyter nbextension enable --py --user d3networkx_psctb

macOS (Mac OS X)

macOS requires the manual installation of PySCeS and Maxima. While OS X comes pre-installed with Python 2.7, Python 3.x is needed and we recommend installing a Python distribution such as Anaconda as it will take care of many of the SciPy stack requirements. Installation was tested on macOS High Sierra.

Python

One of the easiest ways to get Python on your system is to install the Anaconda Python distribution (https://www.anaconda.com/products/individual#Downloads). Download either of the Python 3.7 installers for macOS from the download page and follow the provided instructions.

If you prefer more fine-grained control, there are other options such as installing directly from Python.org (https://www.python.org/downloads/mac-osx/), or installing Homebrew and then installing Python 3.7 with Homebrew. These are advanced options for experienced users, and if you are starting out, we recommend Anaconda!

PySCeS

Binary packages are available for Anaconda, and binary wheels are available for direct installation with pip. Depending on your Python installation (see above), the process is similar to the Windows install.

For Anaconda:

conda install -c sbmlteam -c pysces pysces

For a pip based install (Python versions 3.6-3.8 are supported):

pip install pysces

Maxima

Maxima is necessary for generating control coefficient expressions using SymCA. The latest version of Maxima can be downloaded and installed from the MacOS download page at http://maxima.sourceforge.net/download.html. We recommend the VTK version of Maxima.

After downloading and installing the Maxima dmg, the following lines must be added to your .bash_profile file:

export M_PREFIX=/Applications/Maxima.app/Contents/Resources/opt
export PYTHONPATH=${M_PREFIX}/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/:$PYTHONPATH
export MANPATH=${M_PREFIX}/share/man:$MANPATH
export PATH=${M_PREFIX}/bin:$PATH
alias maxima=rmaxima

PySCeSToolbox

Now you are ready to install PySCeSToolbox. If you are using Anaconda, open up a terminal in the Anaconda environment where PySCeS is installed. For pip based installations, just open up a Terminal. Execute the command:

pip install pyscestoolbox

This will automatically download both PySCeSToolbox and any outstanding requirements.

Note

You may encounter an error during the installation of PySCeSToolbox relating to the removal of temporary files on OS X or macOS. This does not impact on the functioning of PySCeSToolbox at all, and we mean to address this bug in the future.

Enabling widgets

If you are running the Jupyter notebook for the first time, or if you have not yet enabled the notebook widgets you may need to run the following command:

jupyter nbextension enable --py --sys-prefix widgetsnbextension

We also recommend running the following two commands to enable the ModelGraph functionality of PySCeSToolbox. Rerunning this command may be necessary when updating/reinstalling PySCeSToolbox.

jupyter nbextension install --py --user d3networkx_psctb
jupyter nbextension enable --py --user d3networkx_psctb

Linux

Linux requires the manual installation Maxima and PySCeS. Most Linux systems come pre-installed with a version of Python 3.x or it is available from the distribution repositories. However, a Python distribution such as Anaconda may be used instead. Installation was tested on Ubuntu 18.04.

Python

We assume that your system comes with Python 3.x (versions 3.6-3.8 are recommended) and with pip (necessary for installing Python packages that are not available in your OS’s repositories). In case pip is not yet installed, it may be installed from your OS’s repositories or by following the instructions found at https://pip.pypa.io/en/stable/installing/.

If you prefer Anaconda, Linux installers are available here.

PySCeS

Binary packages are available for Anaconda, and binary wheels are available for direct installation with pip. Depending on your Python installation (see above), the process is similar to the Windows and macOS installs.

For Anaconda:

conda install -c sbmlteam -c pysces pysces

For a pip based install (Python versions 3.6-3.8 are supported):

pip install pysces

Maxima

Maxima is necessary for generating control coefficient expressions using SymCA. Maxima can be installed from your repositories, if available, otherwise the latest packages can be downloaded from the Linux link at http://maxima.sourceforge.net/download.html.

PySCeSToolbox

Now you are ready to install PySCeSToolbox. Open a terminal in the environment where you installed PySCeS (i.e. Anaconda environment or the native Python environment of your OS), and simply type in and execute the command:

pip install pyscestoolbox

Enabling widgets

If you are running the Jupyter notebook for the first time, or if you have not yet enabled the notebook widgets you may need to run the following command:

jupyter nbextension enable --py --sys-prefix widgetsnbextension

We also recommend running the following two commands to enable the ModelGraph functionality of PySCeSToolbox. Rerunning this command may be necessary when updating/reinstalling PySCeSToolbox.

jupyter nbextension install --py --user d3networkx_psctb
jupyter nbextension enable --py --user d3networkx_psctb