Webinar: Pathfinders – Biomolecular Simulation

Webinar: Pathfinders – Biomolecular Simulation

This webinar continues our look at our pathfinder activities in the current phase. The subject of this webinar is pathfinder 4 which focuses on process orchestration in Biomolecular Simulation. This webinar will be presented by James Gebbie and Jas Kalayan.

The recording of this webinar is now available on Youtube.

FAIR Data for the Biomolecular Simulation Community


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 the recording of this webinar via our youtube channel.

The pathfinders aim to focus development in strategic areas with the aim to explore and establish exemplar systems that can be brought under the PSDI umbrella and act as templates for future phases of the project. For those that wish to get some more information about the pathfinders before the webinar please go to: https://www.psdi.ac.uk/current-work/wp4-pathfinders/

The PSDI team looks forward to seeing you at the webinar, if you have any questions you can always get in contact with us.

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