WebplatforMD – Integrated Web-based Interactive Data Platform for Molecular Dynamics Simulations

WebplatforMD, an integrated web-based interactive data platform for molecular dynamics simulations, has proved vital for current and future scientific discoveries in Armenia. The platform provides data repository and workflow services and interactive data visualization. It uses datasets generated by various Life Science communities in Armenia. The integrated data platform is presented as an advanced integrated environment to capture, analyze, process and visualize the scientific data.


Figure 1. A web interface for molecules visualization.

The life science communities in Armenia producing significant amount of data and using HPC resources are the Bioinformatics Group of the International Scientific and Educational Center of the National Academy of Sciences of the Republic of Armenia (Bioinformatics group)* and the molecular physics department of the Yerevan State University (MolPhys YSU)**.

The integrated web-based interactive data platform (see Diagram in Figure 2.) allows users to access different services by enabling storage and management of the diverse simulations’ output data and assigning of meta-data to each output in order to increase data reliability. Moreover, the platform allows system searching and downloading for further use. An interactive web-based solution is provided for visualization of the molecule structure via the use of a web browser. Additionally, a public link is provided to enable data downloading for users that do not possess an account on the Integrated Rule-Oriented Data System (iRODS).


Figure 2. Diagram of the integrated web-based interactive data platform.

The deployed infrastructure opens opportunities for biologists in Armenia and beyond to increase the visibility of the actual laboratory processes, to examine the processes’ impact and correlations, and the activities that have more influence on the whole process. It also enables understanding of the relation of the small processes in a larger system and how these interact with each other. Having a single point for all distributed data in Armenia enables researchers to collaborate more efficiently and to share their knowledge.

*   http://www.bioinformatics.am

** http://www.ysu.am

#   https://irods.org/