MDverse

MDverse is an international project aiming at indexing, annotating and exploring molecular dynamics simulation data with the ultimate goal of making it reusable.

💡 Did you know?
1 % of all data stored in the data repository Zenodo is related to molecular dynamics simulations?

Achievements

Data collection: about 250,000 files and 2,000 datasets have been indexed so far. All data are shared as Parquet files under Creative Commons Attribution 4.0 International (CC BY 4.0) license.

MDverse data explorer is a prototype search engine for molecular dynamics data. Browse collected files and search for specific data using keywords.

Preprint: MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations, bioRxiv, 2023.

Paper: MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations, eLife, 2023.

📝 The “Dark Matter of Molecular Dynamics Simulations” refers to data that is technically accessible, but neither indexed, curated, or easily searchable.

Developments

All developments are open-source, available on GitHub and archived in Software Heritage:

• MDverse web scrapper: index and collect molecular dynamaics files from generic data repositories (Zenodo, Figshare and Open Science Framework). Download and mine .mdp and .gro Gromacs files.
• MDverse data analysis: analyze MD data previously collected by the web scrapper.
• MDverse data explorer: prototype search engine for MD data.