There are two different ways to install and use PySB:
- Install PySB natively on your computer (recommended).
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.
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
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.
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 and move it into
/usr/local/share (Mac 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
4. Install PySB
The installation is very straightforward with
pip - type the
following in a terminal:
pip install pysb
Mac users: To open a terminal on a Mac, open Spotlight search (press command key and space), type
terminaland press enter.
5. Start Python and PySB
If you installed Python using Anaconda on Windows, search for and
IPython from your Start Menu (Windows). Otherwise, open a terminal
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!
Recommended additional software
The following software is not required for the basic operation of PySB, but provides extra capabilities and features when installed.
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
pip install matplotlib.
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.
An alternate interactive Python shell, much improved over the standard one.
IPython is included with Anaconda. Otherwise, it can be installed
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
KaSa executables. Note that if you
have downloaded the official binary build of KaSim, it will be named something
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 (Mac or Linux).
Option 2: Docker container with PySB and Jupyter Notebook
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
- Install Docker
To use PySB with Docker, first you'll need to install Docker, which can be obtained from http://www.docker.com.
- 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.
- Start the container
Start the Docker container with the following command (on Linux, the command
may need to be prefixed with
docker run -d -p 8888:8888 pysb/pysb
This starts the PySB Docker container with Jupyter notebook and connects it to port 8888.
- 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.
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:
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
- Anaconda: https://www.continuum.io/downloads
- Docker: http://www.docker.org/
- Kappa: http://www.kappalanguage.org/
- Git: http://git-scm.com/
- IPython: http://ipython.org/
- OCaml: http://caml.inria.fr/ocaml/
- GraphViz: http://www.graphviz.org/
- pandas: http://pandas.pydata.org/
- Python: http://www.python.org/
- SciPy: http://www.scipy.org/
- NumPy: http://www.numpy.org/
- SymPy: http://www.sympy.org/
- matplotlib: http://matplotlib.org/
- BioNetGen: http://www.bionetgen.org/
- Perl: http://www.perl.org/