2018 WESTPA Workshop tutorial by Ali Sinan Saglam, uses WESTPA and BioNetGen
This is a mostly self-contained tutorial to run BNG simulations coupled with WESTPA and some example analysis that can be done.
Instructions:
- For this tutorial you will need:
- Anaconda python distribution
- WESTPA
- PyEMMA
- BioNetGen. A statically compiled binary is included in this tutorial.
- Once you have the requirements installed, clone this repo under westpa/lib/examples folder
- If you have WESTPA installed correctly (e.g. ran setup.sh) the example should run after ./init.sh and ./run.sh
- You should specify the number of cores you want the example to use with ./run.sh --n-workers X, where X is the number of cores you want used.
- Once the simulation is done you can go to the analysis folder and run all analysis for this tutorial with ./run_all_analysis.sh
- Additionally you can go to do the analysis folder and start a jupyter notebook in that folder for the analysis tutorial as well.