The suggested python distribution to use is the Anaconda python distribution. After that is installed, you can install webng directly from PyPI using pip
pip install webng
which will also install WESTPA and BioNetGen python libraries which means you only need to run this command and have your model to run a WESTPA simulation. Please note that Windows is not currently supported.
Common installation issues
If you are using WsL, you will need libncurses5, you can install it with
sudo apt-get install libncurses5
If the webng dependencies don’t automatically install, you can clone the webng repository with
git clone https://github.com/ASinanSaglam/webng.git
and install the repo locally with
cd webng pip install -r requirements.txt pip install -e .
which should install everything you need.
After installation complete you can test to see if it’s properly installed with
if this command prints out help, the command line tool is installed.
In order to use the tool, you will need a YAML configuration file. This tool comes with a subcommand that can generate a template YAML configuration file for you with the command
webng template -i mymodel.bngl -o mysim.yaml
this should write a sample configuration file to
mysim.yaml. See Configuration Options page to
learn more about what is contained in this file. Next let’s actually make the WESTPA simulation
webng setup --opts mysim.yaml
this will create a folder that corresponds to
You can now initialize the simulation with
cd mymodel ./init.sh
if this command completes successfuly you are ready to run your WESTPA simulation. You can run the simulation using a single core with
or you can use multiple cores with the command
w_run --n-workers X
X is the number of cores you want to use. In order to extend the simulation further you
will have to edit
west.cfg file, please read WESTPA tutorials
to learn how to run and manage these simulations.
See Analysis page to learn more about the available analyses in webng.