Quick Start

Installation

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.

Usage

After installation complete you can test to see if it’s properly installed with

webng -h

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 folder with

webng setup --opts mysim.yaml

this will create a folder that corresponds to sim_name in mysim.yaml file. 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

w_run --serial

or you can use multiple cores with the command

w_run --n-workers X

where 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.