Please Note: further content e.g. recordings, slides etc. will be added after the townhall has concluded
We use computer simulations to understand complex biological problems for areas like:
Drug discovery, Protein function, Antimicrobial resistance, Toxicology and Air Quality and many more…
The computer simulations are made up of complex workflows with many steps and look different for different biology.
Currently, it is difficult to reproduce biomolecular simulations, even when work is published and researchers use computational tools. There are a wide range of tools and hardware platforms available and not a consistent approach to how simulation data is stored and shared. Even publications where simulations are well described, are difficult to reproduce due to full provenance of model creation not being present.
This work explores the development of easy-to-use provenance tools to save all simulation steps, with minimal impact to research time.
- Production of AiiDA plugins for provenance capture from GROMACS and Amber simulation engines
- Development of online database for storing workflows
Some of this work can be explored through the townhall poster, which shows the wider vision of the work as well as a specific case study ‘Towards Building a GPCR Lipid Fingerprint Dataset’. Alongside this are the aiida-gromacs and aiida-amber plugins with their guidance documentation and a tutorial + demo for aiida-gromacs which the users can walk through themselves.
The Team members at the June Townhall
James Gebbie
Jas Kalayan
Previous presentations to PSDI
The work in this pathfinder was previously presented as a PSDI webinar, although the work has progressed since that presentation it provides a useful overview of the work and a demonstration of some of the capabilities.
Youtube link to video: https://www.youtube.com/watch?v=FA_rVv-hZig
Link to Slides: https://doi.org/10.5281/zenodo.10462078