[Vision] Fwd: NBCR Tech Mini Series on Distributed Real Time Visualization of Computational Simulation and Workflows, Sept 23, 2009

Wilfred Li wilfred at sdsc.edu
Wed Sep 23 08:08:55 PDT 2009

From: Wilfred Li <wilfred at ad.sdsc.edu<mailto:wilfred at ad.sdsc.edu>>
Date: September 23, 2009 7:38:15 AM PDT
To: "support at nbcr.net<mailto:support at nbcr.net>" <support at nbcr.net<mailto:support at nbcr.net>>
Subject: NBCR Tech Mini Series on Distributed Real Time Visualization of Computational Simulation and Workflows, Sept 23, 2009

NBCR Tech Mini Series on

Distributed Real Time Visualization of Computational Simulation and Workflows,

Date: Today, Sept. 23, 2009

Time: 10 am to 12 pm

Location: Room 3004, Atkinson Hall, UCSD

Refreshments provided.

Distributed Real Time Visualization of Computational Simulation and Workflows, Sep 23 2009
Real Time Frame-based Biomedical Data Streaming

Kejun Kevin Dong, Ph.D.

Biomedical research often involves receiving and analyzing gigabytes to terabytes of data, generated by scientific instruments and applications from the grid/cloud computing environment. For biomedical scientists conducting simulation experiments, they currently have to wait for days to months to visualize and analyze their frame-based data. To enhance the ability to see and analyze their data in real time, we have developed a system to monitor and visualize the on-going simulation experiments. We have developed the support for molecular dynamic simulation software, e.g. NAMD, by streaming data frames from supercomputers to various clients, using the RBNB dataturbine middleware. A prototype RBNB dataturbine cloud has been set up, consisting of RBNB dataturbine servers at NBCR (vm5.ucsd.edu<http://vm5.ucsd.edu/>) and CNIC (dt.escience.cn<http://dt.escience.cn/>), for the biomedical data streaming service. For visualization, ours data turbine service supports visualization using an extended version of JMol (http://jmol.sourceforge.net/) software, an open-source Java viewer for chemical structures in 3D, to fetch pdb frames from RBNB dataturbine servers and realize sink-enabled web-based 3D visualization. Other visualization environments such as the Realtime Data Viewer (RDV), Cave Automatic Virtual Environment (CAVE), and Tile Display Walls may be supported with customized plugins.

Vision-based Workflow environment for Accessing Opal-enabled Scientific Software as a Service (SaaS)

Jane Ren

Vision is a Python based workflow environment with a visual programming interface. We have recently developed a computational workflow using Vision nodes to support Computer Aided Drug Discovery (CADD), using a service oriented computing architecture. Key applications such as PDB2PQR, AutoDock are deployed as Opal-enabled web services with a scalable computing backend, using cluster or cloud computing services. Recently, the metascheduler CSF4 has been integrated into the CADD workflow to distribute virtual screening experiments at sites in Japan and the US, part of the PRAGMA grid. Vision nodes for NAMD simulation using the TeraGrid resources are also under development, and a prototype environment using the CSF4 to send NAMD simulation to the TeraGrid has been established. In this talk, the progress towards supporting the Relaxed Complex Scheme (RCS) using NAMD and AutoDock using the Vision workflow environment will be reported. Future support for real time visualization of MD and docking simulations will be discussed.

Visualization of MD Trajectories on the CAVE and Tiled Display Wall using COVISE

Kevin Wu

Molecular dyamics (MD) trajectories are data from simulation experiments of molecular interactions over a predefined time scale achievable with available computational resources over a period of time. MD simulations may be used to model biological systems such as protein ligand interactions under solvated conditions. They may be applied in conjunction with other computational methods such as the Relaxed Complex Scheme (RCS) for drug discovery and investigation of host pathogen interactions. The scientists would benifit from examining the data within a thorough, immersive, and in depth viewing environment of the simulation in real time, and at different locations for collaborative discovery. We present the progress on the development of a customized plugin for real time visualization of MD trajectory data using the COllaborative VIsualization and Simulation Environment (COVISE) in the StarCAVE and the Tiled Display Wall (TDW). This plugin uses a ringbuffer system to retrieve frame-based data from a dataturbine server, and display the information in 3D.

Host: Wilfred W. Li, Ph.D.

Contact: 858 534 0591

Additional information available at

About NBCR: Established in 1994 with funding (P41 RR08605) from the
National Center for Research Resources (NCRR), NIH, the overall mission
of the National Biomedical Computation Resource (NBCR) is to conduct,
catalyze and enable multiscale biomedical research by harnessing
forefront computational and information technologies. The five key
objectives of NBCR are as follows: i) Push forward the frontiers of
integrative, multiscale modeling. ii) Accelerate the adoption and
development of emerging information technologies by the biomedical
science community. iii) Focus new activities on translational medicine
related to the NIH mission. iv) Strengthen the multidisciplinarity of
the Resource. v) Expand service, training and dissemination.

Best Regards,


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