A Scientific Gateway for the hydrodynamic analysis of macromolecules with UltraScan
PI: Borries Demeler, UTHSCSA
Science Gateways Group, Visualization and Analytics, UITS Research Technologies
This project aims to further develop a science gateway that has enabled over 100 scientists during the past year to perform sophisticated, high-resolution hydrodynamic modeling of biological macromolecules and synthetic polymers using the UltraScan software. The analysis is performed on remote supercomputers. The gateway allows scientists to easily interact with the remote supercomputer through a web interface, and to store their data in a remote database. The gateway also provides access to their data and analysis reports from anywhere through a web interface, and to collaborate with others on their research projects. Our gateway has seen dramatic increase in usage, as approximately 30 new laboratories were added. In 2011, 24 users analyzed 3300 samples. In 2012, 99 users analyzed 8050 samples, while in the first 3 quarters of this year we saw 105 users and 14,730 samples analyzed, and we integrated a European supercomputer (Juropa) into our gateway. Extended collaborative support from XSEDE staff at Indiana University has been essential for this outcome.
The UltraScan science gateway provides the highest resolution analysis available for analytical ultracentrifugation experimental data. Such experiments are of integral importance in many research projects in biochemistry, microbiology, material science, biomedical applications, nanotechnology, synthetic polymer science, and other fields where study of solution properties of macromolecules is essential. Because of the use of supercomputers enabled through the NSF/XSEDE infrastructure, investigators can perform exceptionally detailed analyses in all of these fields. Consequently, the UltraScan software has been used for many studies reported in peer-reviewed manuscripts. Over 300 citations have been deposited in the UltraScan reference database (http://www.ultrascan.uthscsa.edu/searchrefs.php), citing UltraScan for their data analysis.
Analytical ultracentrifugation experiments and related techniques help scientists understand the properties of large molecules and nanoparticles in solution. Such an environment best reveals the dynamics between interacting systems. The analysis is computationally very expensive and demands high performance computing resources. The UltraScan Science Gateway helps experimental scientists use these complex resources through a simple user interface to analyze their data. Prof. Borries Demeler at UTHSCSA is the PI and principal architect of the UltraScan science gateway infrastructure, and conducts regular workshops to disseminate the open source UltraScan software and train new users. He is supported by NSF Grant NSF-DAC-1339649.
Images: Increase in usage of the UltraScan-III Science Gateway facilitated by XSEDE/NSF since inception in 2011. Shown are number of compute cycles used on XSEDE and other resources combined (green), number of investigators taking advantage of the UltraScan Science Gateway to analyze their samples (red), and number of analyses performed (blue). Please note: Data for 2013 are projected from 10/13 until the end of the year based on data currently available.
NSF GSS Codes:
Primary Field: Geosciences (302) Hydrology and Water Resources Sciences
Secondary Field: Computer Science (401) Data Modeling