MDverse data analysis

Setup your environment

Clone the repository:

git clone https://github.com/MDverse/mdda.git

Move to the new directory:

cd mdda

Install miniconda.

Install mamba:

conda install mamba -n base -c conda-forge

Create the mdda conda environment:

mamba env create -f binder/environment.yml

Load the mdda conda environment:

conda activate mdda

Note: you can also update the conda environment with:

mamba env update -f binder/environment.yml

To deactivate an active environment, use

conda deactivate

Get data

Run this command to download required data files:

bash scripts/get_data.sh

Files are downloaded in the data directory:

$ tree data
data/
├── data_model_parquet.md
├── datasets.parquet
├── files.parquet
├── gromacs_gro_files.parquet
├── gromacs_mdp_files.parquet
└── gromacs_xtc_files.parquet

The data model is described in the codebook data/data_model_parquet.md

Analyse data

Use this script to run all Jupyter notebooks in batch mode:

bash make_results.sh

The directory results contains Jupyter notebooks exported in html, figures as .png and .svg images and a couple of TSV files. All these files are also bundled in the results.zip file.