Past Events

This online talk is part of the  DRIIMB webinar series and will be given by  Dr Jas Kalayan from STFC, UKRI.

Registration is free but required - Click here to register!

Title:  BioSimDR: a Collection of Data Tools and Infrastructure for Biomolecular Simulation

Abstract: BioSimDR (BioSim Data Resources) [1] are data tools and prototype services specifically built to enable FAIR data sharing in biomolecular simulation communities (CCPBioSim [2] and HECBioSim [3]) based in the UK and is funded by the Physical Sciences Data Infrastructure (PSDI) [4].

Molecular dynamics simulations give atomic-scale insights into the complex interactions and dynamics of flexible biological systems. It is often difficult to access and interpret ensembles of flexible molecules from experiments, consequently, integration of simulations and experiments can improve flexible fitting of simulations to experimental data. Accessibility of simulation protocols and data remains a challenge and impedes efforts to open accessibility of simulations to more researchers.

To produce meaningful biomolecular simulations, careful consideration of the tools used, and parameters selected for each step performed is required. With numerous decisions and options, it is often too convoluted to describe all simulation steps in scientific articles. However, this leaves a knowledge gap between the originators and other curious researchers, leading to inconsistencies in reusing simulations deposited in data repositories.

BioSimDR aims to address these shortcomings in how simulation data is stored, shared, and reused, with consensus from the BioSim community. To assist in data storage and sharing, we present BioSimDB, a prototype data repository dedicated to biomolecular simulations. To address data reuse, we present tools to collect simulation provenance and metadata, where simulators can record every simulation step as it is executed, which can be easily bundled and shared to BioSimDB.

[1] https://resources.psdi.ac.uk/resource-theme/b01dc999-4bb5-49d8-8a45-23cef457d6b4

[2] https://www.ccpbiosim.ac.uk/

[3] https://www.hecbiosim.ac.uk/

[4] https://www.psdi.ac.uk/