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==2008==
===Supercomputing conference at Austin, Texas===

Booth 3306, coordinated by [http://www.nbcr.net/events/supercomputing/2008 NBCR]

====Schedule at a glance====

{| class="wikitable" style="width:75%; height: 200px" border="1"
|-
! Time\Date
! Monday, Nov 17, 2008
! Tuesday, Nov 18, 2008
! Wednesday, Nov 19, 2008
! Thursday, Nov 20, 2008
|-
| 10:00 - 11:00 am
|
| NBCR
| NCMIR
| NBCR
|-
| 11:00 - 12:00 pm
|
| NCMIR
| NBCR/PRIME
| NRBSC
|-
| 12:00 - 1:00 pm
| 
| NRCAM
| NBCR/PRIME
| NBCR
|-
| 1:00 - 2:00 pm
| 
| TCBG
| TCBG
| NBCR
|-
| 2:00 - 3:00 pm
| 
| TCBG
| TCBG
| TCBG
|-
| 3:00 - 4:00 pm
|
| CIBC
| CIBC
| NBCR
|-
| 4:00 - 5:00 pm
|
| CIBC
| CIBC
|-
| 5:00 - 6:00 pm
|
| NBCR
| NBCR
|-
| 6:00 - 7:00 pm
| NRCAM
|-
| 7:00 - 8:00 pm
| CIBC
|-
| 8:00 - 9:00 pm
| NBCR
|}

====Title, Abstract and Presenters====

=====Exploring Biomolecular Machines with Supercomputers and GPUs=====

James Phillips and John Stone

The NIH Resource for Macromolecular Modeling and Bioinformatics and Theoretical and Computational Biophysics Group is located at the Beckman Institute of the University of Illinois at Urbana-Champaign.  
The Resource brings advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance through direct collaboration with experimental researchers, the distribution of user-friendly cutting-edge software, and a broad range of training and dissemination activities.

The flagship software packages NAMD and VMD, both distributed free of charge with source code, facilitate the discovery process from analysis, through modeling, to visualization of the molecular apparatus in biological cells:
 * NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular 
   dynamics code used regularly to simulate systems of 1,000,000 atoms and 
   beyond on both large supercomputers and inexpensive Linux clusters.

 * VMD is a molecular visualization program for displaying, animating, 
   and analyzing large biomolecular systems using hardware-accelerated 
   3-D graphics and built-in scripting.

Both packages have been adapted for GPU acceleration using the CUDA programming system from NVIDIA.  This work is described at SC08 in tutorial M02, "High Performance Computing with CUDA" (all day Monday), and technical paper 323, "Adapting a Message-Driven Parallel Application to GPU-Accelerated Clusters" (Tuesday, 11:30pm-12pm, Ballroom E).  
Demos may be viewed at the NVIDIA and Sun booths.

=====Vision based workflow management for computer aided drug discovery=====

Luca Clementi and Wilfred Li

co-authors: Sriram Krishnan, Guillaume Vareille, Jane Ren, Wes Goodman, Michel Sanner, Peter Arzberger

The Avian Flu Grid is a virtual organization dedicated to the discovery of novel inhibitors for the pandemic avian flu threat,
leveraging grid technologies and computational resources provided by
PRAGMA and its partners. In this context it is essential to adopt
tools which increase the productivity of the computational
scientists without advanced training on grid technologies. To
reduce the learning curve, we have augmented tools that most
domain scientists are already familiar with such as AutoDock and AutoDockTools, and hidden the complexity
of the underlaying infrastructure, through automatic user interface
generation and workflow support, beyond the standard command line
based approach. We present the current state of the
infrastructure deployed and how it has facilitated the training of
new researchers in the drug discovery area. We provide details on
Vision, a visual programming environment used to define scientific
workflows, and Opal, an automatic Web service wrappers for
scientific applications on Grid resources, and how they are
integrated with other established back-end technologies.

=====Optimized Rendering for a Three-Dimensional Videoconferencing System=====

Presenters:
Rachel Chu
rchu@ucsd.edu
Daniel Tenedorio
dtenedor@ucsd.edu 

Co-Authors: 
Jurgen Schulze, UCSD
Susumu Date, Seiki Kuwabara, Atsushi Nakazawa, Haruo Takemura, Osaka University Fang-Pang Lin, National Center for High-performance Computing


Two-dimensional videoconferencing systems abound in industry and government. Unfortunately, technological limitations prevent them from enjoying more widespread use. We aim to revolutionize telepresence by bringing a three-dimensional videoconferencing system one step closer to reality by optimizing various stages of the rendering pipeline. The system begins with the capturing stage, in which one person stands in a designated area that is encircled by cameras. While the cameras take footage of the person speaking, a computer cluster generates real-time 3D data in the form of point clouds, or large collections of 3D coordinates and colors. Once the cluster generates each point cloud, it sends it over a fast network to another location.

Here, a receiving computer analyzes the cloud and uses a newly discovered algorithm to resample it, producing a smaller, more manageable data set that can be rendered within acceptable time constraints. Then, a parallel rendering system takes over. A master computer partitions the data set into small groups, and sends each group to one of sixteen high-definition projectors to be displayed. The projectors display onto each of four walls, forming a cube (there are back, left, right, and ground screens). The projectors are organized into eight groups of two; each pair projects onto half of one screen, using orthogonally polarized filters. The viewer then stands in the cube and wears a set of polarized 3D glasses, where each eye sees of one the two projectors. The brain combines the two similar images, creating the illusion of depth. Finally, a head tracking system monitors the real-time location of the viewer, sending position data back to the master node, which updates the rendered images accordingly.

=====Using a Grid Enabled, Virtual Screening Platform to Discover Unique Inhibitors for SSH-2=====

Phillip D. Pham, Marshall J. Levesque, Kohei Ichikawa, Susumu Date, Jason H. Haga

The slingshot-2 (SSH-2) protein plays a key role in certain cellular processes, namely cellular motility and growth. SSH-2 is a member of a specific class of enzymes called dual specificity phosphatases (DSPs). DSPs are defined by a similar function of targeting the phosphothreonine and phosphotyrosine residues of mitogen-activated protein (MAP) kinases, which regulate cell growth. Because DSPs share a common function and structure, it is of great interest to determine a unique inhibitor for a DSP, such as SSH-2, to gain tools that will help further the understanding of cellular processes. Through the implementation of an in silico procedure of screening a large database of chemical compounds against SSH-2 employing grid technologies and the molecular docking software DOCK 6, several chemical compounds have been identified as potential inhibitors of SSH-2 activity. The relative degree of specificity among the select inhibitors was characterized based on energy score rankings as well as compound structure. Grid performance issues will also be presented. Consensus energy score rankings from the 0.3-Å and AMBER DOCK screenings indicated that 2-amino-3-phosphonooxy-propanoic acid had the most potential, which will be verified with wet bench testing.

=====Virtual Screening Using Grid Computing for Specific SHP-2 Inhibitors=====

Simon X. Han, Marshall J. Levesque, Kohei Ichikawa, Susumu Date, Jason H. Haga

Virtual screening is the use of computer algorithms to compute protein-substrate affinity. Utilizing the multi-institutional PRAGMA Grid computation resources, we have screened the ZINC 7 substrate database against SHP-2 using the virtual screening software DOCK 6.2. Complications occurred in the multiple and repeated screenings on the grid and potential improvements will be discussed. SHP-2 is a protein tyrosine phosphatase that has important cellular functions such as development, growth, and death. It has thus been hypothesized to be involved in many disease pathways such as that of diabetes, Alzheimer’s, and cancer. In this study, we have identified a list of potential SHP-2 specific inhibitors that can be further tested and validated in a laboratory. The knowledge gained can help better understand the disease pathways SHP-2 is involved in and has future clinical significance in creating new drug therapies that treat those diseases.