Readme

Supporting code for Bayesian Transporter research - still under development.

Getting started

• create an environment with required packages/dependencies using conda env create -f environment.yml
• run through the example_notebook.ipynb notebook for example usage and analysis
  • ensure that the filepaths are correctly set for your system in the configuration file ...config.yaml configuration file.
• an \example directory is included in the repo which contains data from a short pocomc sampling run, along with an example configuration file, SBML and tellurium transporter model, and synthetic observed dataset.

Stand alone usage

• For Bayesian inference using EMCEE run python YOUR_PATH_HERE/run_emcee.py in a terminal
• For Bayesian inference using PocoMC run python YOUR_PATH_HERE/run_pocomc.py in a terminal
• For Maximum Likelihood Estimation using Scipy Optimization run python YOUR_PATH_HERE/run_optimizer.py.py in a terminal

Ensure that the configuration file and file path is updated for each module as needed

Limitations / issues

• parallelization issues with libroadrunner. see: sys-bio/tellurium#563
• pocoMC sampler bugs, use my fork with fix. see: minaskar/pocomc#22 and my fork: https://github.com/augeorge/pocomc

Docs

More detailed API documentation is provided below:

• https://zuckermanlab.github.io/Bayesian_Transporter/

August George, 2023