Skip to main content

FAIR Data for the Biomolecular Simulation Community

This webinar discusses reproducible data in Biomolecular Simulation.

About the Webinar​

Welcome to the Physical Sciences Data Infrastructure (PSDI) webinar series. This webinar series is designed to communicate the PSDI work to a wider audience!

The subject of this webinar is our pathfinder focused on process orchestration in Biomolecular Simulation. This webinar, held on 18th October 2023, was presented by James Gebbie and Jas Kalayan.

The biomolecular simulation community produces vast amounts of data to study complex biological systems at atomic scales. Yet, how we store, share, and reuse our data is not well defined. One problem is that our simulation pipelines are difficult to replicate without detailed descriptions of each step. Another problem is the data files we produce can often be too large to store on the national compute facilities, which most of this data is produced on. In this webinar we present possible solutions to address these two problems; firstly, a software tool to record data provenance towards FAIR [1] compliant formats, and the other an online data repository to store and share this data.

For reproducible data, we utilise the powerful AiiDA Python infrastructure [2,3] to develop our aiida-gromacs plugin [4], for tracking all inputs and outputs from simulation protocols performed with the GROMACS MD engine [5]. We show how aiida-gromacs can be used with minimal changes to how researchers already work, to allow for easy adoption of provenance tools within our community. To address the findable and accessible components of FAIR compliancy, we also briefly present our prototype data infrastructure. Our aim is to allow researchers to directly upload data produced via aiida-gromacs onto our database for easy access, querying and visualisation of simulation data/metadata online. We encourage the biomolecular simulation community to try aiida-gromacs, we have installation guides and tutorials available online. Please have a go, contribute, and provide us with feedback for improving aiida-gromacs!

  1. Wilkinson, Mark D. et al. (2016). Scientific Data, 3(1), 160018.
  2. https://www.aiida.net/sections/about.html
  3. Huber, Sebastiaan P. et al. (2020). Scientific Data, 7(1), 300.
  4. https://aiida-gromacs.readthedocs.io/en/latest/index.html
  5. https://www.gromacs.org/

Watch the recording​

You can watch this recording via our You Tube channel.