Building MDbox: An Open Access Simulation Data Repository on CKAN and AWS
Dr Karmen Condic-Jurkic (right) with Dr Megan O'Mara and Steven De Costa. Image: Stuart Hay, ANU
Showing up in the spotlight of HealthHack in 2015, thanks to the initiative of Dr Karmen Condic-Jurkic, the ANU Research School of Chemistry has recently won funding for the establishment of MDbox — a cloud-based repository and analysis toolkit for molecular dynamics simulations.
"ANU is proud to be at the centre of Australia's innovative economy. The University has produced world-class technology from a base of fundamental research"
Working with the ANU Research School of Chemistry, Link Digital will establish MDbox on Amazon Web Services, initially as a data discovery platform based on CKAN. MDbox will iterate over the months and years ahead to facilitate cloud storage solutions, high performance computational simulations, integrated molecular dynamics analysis tools and meta-analysis tools.
Computational modelling is an essential part of experimental testing in almost every branch of science. It has become increasingly popular in chemistry and biology due to its intrinsic facility to accelerate the selection process of candidates during the design process of therapeutic drugs, catalysts, and materials.
While supercomputer simulations are a great asset to the research process, they are costly to run and can take up a lot of computational cycles over days, weeks and months.
Dr Karmen Condic-Jurkic, a Postdoctoral researcher and one of the project leaders, believes that sharing the already existing simulation data would result in a faster flow of ideas and innovations.
This open data initiative is expected to provide enormous value for both academia and industry by boosting research productivity and creating new opportunities for cross-disciplinary research.
Having solid experience in building Government open data portals , and with a globally recognised CKAN service, Link Digital considers the development of open access platforms to be both an innovative and challenging objective to accomplish.
The establishment of MDbox as a platform for supporting research simulations follows naturally from an earlier collaboration between Link Digital, the NCI (National Computational Infrastructure) and Amazon Web Services to deliver a proof of concept for Raijin in-a-box, funded by Intel in 2015.
For some time now we've been thinking about how to publish the full set of research artifacts needed to replicate and review work undertaken by labs, or to swap out data and reconstitute the research in a new context. MDbox will be a great opportunity for us to expand our established capability in both data discover platforms and the orchestration of clusters for super-computing workloads on Amazon Web Services. I've come to think of this, along with the publishing of code, as a model for friction-less science.
Executive Director of Link Digital, Steven De Costa
Link is thoroughly proud to be part of this Australian innovation and is strongly convinced that MDbox will be a major breakthrough in the area of research chemistry.
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Image credit: Stuart Hay, ANU Ref: http://www.anu.edu.au/news/all-news/innovation-funding-to-boost-anu-research