Pathfinder 4 – FAIR Data for the Biomolecular Simulation Community: webinar recording available

Home » Pathfinder 4 – FAIR Data for the Biomolecular Simulation Community: webinar recording available

Jan 8, 2024

The recording from our fourth PSDI webinar is now available on our Youtube Channel!

In this webinar James Gebbie-Rayet and Jas Kalayan presented about FAIR (findability, accessibility, interoperability, and reusability) data for the Biomolecular Simulation Community as part of Pathfinder 4.

If you weren’t able to attend the webinar live, then check this recording out. The slides are available on zenodo:

Abstract: 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.
[3] Huber, Sebastiaan P. et al. (2020). Scientific Data, 7(1), 300.