HPCViz seminar, December 5, 9.00 – 11.00

Next HPCViz seminar will be held Wednesday December 5: starting at 9:00 in the VIC studio. We are happy to announce the following speakers: Rossen Apostolov and Ali Gholami. See below for more information.

See you there!

 Rossen Apostolov

Title: Ensemble Computing and Markov State Models in Molecular Dynamics Simulations

Molecular Dynamics (MD) simulations are extensively used for atomistic  level studies of structural changes in molecules, inter-molecular interactions, phase transitions etc. A single MD simulation follows the time evolution of a stochastic system and is in practice unable to fully explore all possible states of the system, as needed for achieving statistical significance. The system can reach meta-stable states that  it cannot escape or some events of interest may occur on timescales far beyond what is achievable with current methodology. In addition, most of the supercomputers nowadays have capabilities far beyond the hard-scaling limits of many bio-molecular systems of interest.

Being inherently embarrassingly parallel in nature, ensemble computing presents opportunities for improving the sampling of system states by staging thousands of system replicas to run in parallel. However extracting meaningful information from the vast amount of this trajectory data is not an easy task. Markov State Models (MSM) generate  kinetic
models based on collected large-scale simulation data. They can  help greatly in understanding the evolution of investigated system while allowing to reach timescales larger than those of the individual simulation runs.


Ali Gholami

Title: Security of the Biobank Cloud


Recent improvements in the cost and throughput of DNA sequencing machines have caused a mismatch between the increasing rate at which they can generate genome data and the ability of existing tools and computational infrastructure to both store and analyze this data. Biobank Cloud as a new project in context of 7FP aims to address shortage of storage and computational resources through cloud computing service models. However, EU directives on data protection hinder users and organizations to exploit capabilities of cloud computing. In this seminar, we present the Biobank Cloud security concerns and factors that need to be addressed at both interface and internal level. In addition, we discuss authentication, authorization and  auditing mechanisms that are proven in large scale distributed systems.