Installation

There are two different ways to install and use PySB:

1. Install PySB natively on your computer (recommended).

   OR

2. Download a Docker container with PySB and Jupyter Notebook. If you are familiar with Docker, PySB can be installed from the Docker Hub by typing docker pull pysb/pysb. Further details are below.

Note

Need Help? If you run into any problems with installation, please visit our chat room: https://gitter.im/pysb/pysb

Option 1: Install PySB natively on your computer

1. Install Anaconda

   Our recommended approach is to use Anaconda, which is a distribution of Python containing most of the numeric and scientific software needed to get started. If you are a Mac or Linux user, have used Python before and are comfortable using pip to install software, you may want to skip this step and use your existing Python installation.

   Anaconda has a simple graphical installer which can be downloaded from https://www.continuum.io/downloads - select your operating system and download the Python 2.7 version. The default installer options are usually appropriate.

   Note

   Windows users: If you are unsure whether to use the 32-bit or 64-bit installer, press the Windows Start button, search for “About your PC”, and under “System type” it will specify 32-bit operating system or 64-bit operating system

2. (Windows only) Install perl

   Press the Windows Start button, search for “command prompt”, and select it/press enter. Then enter the following at the prompt:

   conda install --yes perl

   Use the command prompt when you need to type commands in a terminal.

3. Install BioNetGen

   Download BioNetGen from here: http://bionetgen.org/index.php/BioNetGen_Distributions

   Extract the download, rename the unzipped BioNetGen-x.y.z folder to just BioNetGen and move it into /usr/local/share (Mac or Linux) or C:\Program Files (Windows). If you would like to put it somewhere else, set the BNGPATH environment variable to the full path to the BioNetGen-x.y.z folder.

4. Install PySB

   The installation is very straightforward with pip - type the following in a terminal:

   pip install pysb

   Note

   Mac users: To open a terminal on a Mac, open Spotlight search (press command key and space), type terminal and press enter.

5. Start Python and PySB

   If you installed Python using Anaconda on Windows, search for and select IPython from your Start Menu (Windows). Otherwise, open a terminal and type python to get started (or ipython, if installed).

   You will then be at the Python prompt. Type import pysb to try loading PySB. If no error messages appear and the next Python prompt appears, you have succeeded in installing PySB! You can now proceed to the Tutorial.

Recommended additional software

The following software is not required for the basic operation of PySB, but provides extra capabilities and features when installed.

• matplotlib

  This Python package allows you to plot the results of your simulations. It is not a hard requirement of PySB but many of the example scripts use it. matplotlib is included with Anaconda. Otherwise, it can be installed with pip install matplotlib.

• pandas

  This Python package provides extra capabilities for examining large numerical datasets, with statistical summaries and database-like manipulation capabilities. It is not a hard requirement of PySB, but it is a useful addition, particularly with large sets of simulation results. pandas is included with Anaconda. Otherwise, it can be installed with pip install pandas.

• IPython

  An alternate interactive Python shell, much improved over the standard one. IPython is included with Anaconda. Otherwise, it can be installed with pip install ipython.

• Kappa 4.0

  Kappa is a rule-based modeling tool that can produce several useful model visualizations or perform an agent-based model simulation. PySB optionally interfaces with its KaSim simulator and KaSa static analyzer.

  To install Kappa for PySB use, put the KaSim executable (and optionally KaSa if you have it) in /usr/local/share/KaSim (Mac or Linux) or C:\\Program Files\\KaSim (Windows). If you would like to put it somewhere else, set the KAPPAPATH environment variable to the full path to the folder containing the KaSim and KaSa executables. Note that if you have downloaded the official binary build of KaSim, it will be named something like KaSim_4.0_winxp.exe or KaSim_4.0_mac_OSX_10.10. Regardless of where you install it, you will need to rename the file to strip out the version and operating system information so that you have just KaSim.exe (Windows) or KaSim (Mac or Linux).

Option 2: Docker container with PySB and Jupyter Notebook

Background

Docker is a virtualization platform which encapsulates software within a container. It can be thought of like a virtual machine, only it contains just the application software (and supporting dependencies) and not a full operating system stack.

Install Docker and the PySB software stack

1. Install Docker

   To use PySB with Docker, first you’ll need to install Docker, which can be obtained from http://www.docker.com.

2. Download the PySB software stack from the Docker Hub

   On the command line, this requires a single command:

   docker pull pysb/pysb

   This only needs to be done once, or when software updates are required.

3. Start the container

   Start the Docker container with the following command (on Linux, the command may need to be prefixed with sudo):

   docker run -d -p 8888:8888 pysb/pysb

   This starts the PySB Docker container with Jupyter notebook and connects it to port 8888.

4. Open Jupyter Notebook in a web browser

   Open a web browser of your choice and enter the address http://localhost:8888 in the address bar. You should see a web page with the Jupyter notebook logo. Several example and tutorial notebooks are included to get you started.

Important notes

To see graphics from matplotlib within the Jupyter Notebook, you’ll need to set the following option in your notebooks before calling any plot commands:

%matplotlib inline

Any Jupyter notebooks created will be saved in the container itself, rather than on the host computer. Notebooks can be downloaded using the Jupyter interface, or a directory on the host computer can be shared with the container.

The PySB container builds on the Jupyter SciPy notebook, which contains further information on the options available for the container (such as sharing a directory with the host computer to preserve notebooks, setting a password and more). Documentation from the Jupyter project is available at https://github.com/jupyter/docker-stacks/tree/master/scipy-notebook