Emre Brookes
Suresh Marru
ABSTRACT
UltraScan Solution Modeler (US-SOMO) computes hydrodynamic parameters and small-angle scattering data from biological macromolecular structural representations and compares them with experimental data for structural determination and validation. At XSEDE 12, a GUI integrated gateway was introduced to offload large computations to various HPC resources. The gateway was directly integrated into the Qt/GUI based software to allow the users a seamless experience. The software is available as source code or precompiled for Apple Mac OSX, MS-Windows and Linux. Current cluster resources include TACC Lonestar and Stampede, SDSC Trestles and a 256 CPU cluster local to the University of Texas Health Science Center at San Antonio. The simplicity of design allowed the implementation of a new method of modeling small angle scattering data that provided new scientific insights and was presented at the 2012 international small-angle scattering conference. Since introduction, multiple workshops have been taught and users are beginning to utilize the gateway in their biological research.
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- Brookes, E, Singh, R, Pierce, M, Marru, S, Demeler, B, and Rocco, M. 2012. Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools. XSEDE '12. ACM, New York, NY, USA, Article 42, 8 pages. DOI=10.1145/2335755.2335839 Google ScholarDigital Library
- Brookes, E, Demeler B, Rosano, C, and Rocco, M. 2010. The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule. European Biophysics Journal, 39:423--5Google ScholarCross Ref
- Rai, N, et al., SOMO (SOlution MOdeler): Difference between x-ray and nmr-derived bead models suggest a role for side chain flexibility in protein hydrodynamics. Structure 13, 723--734, 2005Google ScholarCross Ref
- Demeler, B. 2005. UltraScan: a comprehensive data analysis software package for analytical ultracentrifugation experiments. Modern AUC: Techniques and Methods. Scott, D. J. et al., Eds. Royal Society of Chemistry 210--9Google Scholar
- UltraScan. http:/www.ultrascan.uthscsa.eduGoogle Scholar
- Qt. http://qt.nokia.comGoogle Scholar
- Trac. http://trac.edgewall.org/Google Scholar
- Pierce, M., S. Marru, et al. 2010. Open grid computing environments: advanced gateway support activities. Proceedings of the TG10 Conference, ACM: 16:11--16:19. Google ScholarDigital Library
- 20th International AUC Symposium. http://auc2012.uthscsa.edu/Google Scholar
- The Research Complex at Harwell. http://www.rc-harwell.ac.uk/Google Scholar
- Intl. Small-angle Scattering Conf. http://www.sas2012.comGoogle Scholar
Index Terms
- US-SOMO cluster methods: year one perspective
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