km-stats

Statistical models of kinetic parameter data from the BRENDA and SABIO-RK databases.

Fetching data

Raw data can be found in the folder data/raw/.

This data was fetched using the script fetch_data.py. In order to run this script, you will need to register with BRENDA and set environment variables BRENDA_EMAIL and BRENDA_PASSWORD appropriately. You will also need to install the python packages zeep and tqdm.

Requirements

To install python dependencies run this terminal command in a suitable environment (python 3.7 or higher should work)

pip install -r requirements.txt

Note that this repository depends on cmdstanpy, which in turn has non-python dependencies. See here for details about how to install these.

Reproducing our results

Our results can be reproduced by running the command make results from the project's root directory.

Individual components of the analysis can be reproduced by running the relevant python scripts:

python fetch_data.py  # this takes a long time
python prepare_data.py
python generate_results.py
python analyse.py

Investigating the results

To investigate the results of a the blk model run, ensure that the file results/runs/blk/posterior/idata.nc exists and then start our webapp with the following command:

streamlit run app.py