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Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools

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dc.contributor.author Brookes, Emre
dc.contributor.author Singh, Raminderjeet
dc.contributor.author Pierce, Marlon
dc.contributor.author Marru, Suresh
dc.contributor.author Demeler, Borries
dc.contributor.author Rocco, Mattia
dc.date.accessioned 2012-10-10T14:46:38Z
dc.date.available 2012-10-10T14:46:38Z
dc.date.issued 2012
dc.identifier.citation Emre Brookes, Raminderjeet Singh, Marlon Pierce, Suresh Marru, Borries Demeler, and Mattia Rocco. 2012. Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools. In Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the campus and beyond (XSEDE '12). ACM, New York, NY, USA, , Article 42 , 8 pages. DOI=10.1145/2335755.2335839 http://doi.acm.org/10.1145/2335755.2335839 en_US
dc.identifier.uri http://doi.acm.org/10.1145/2335755.2335839 en_US
dc.identifier.uri http://hdl.handle.net/2022/14723
dc.description This is a preprint of a paper in the proceedings of the XSEDE12 conference, held July 16-19, 2012 in Chicago, IL. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. en_US
dc.description.abstract UltraScan Solution Modeler (US-SOMO) processes atomic and lower-resolution bead model representations of biological and other macromolecules to compute various hydrodynamic parameters, such as the sedimentation and diffusion coefficients, relaxation times and intrinsic viscosity, and small angle scattering curves, that contribute to our understanding of molecular structure in solution. Knowledge of biological macromolecules' structure aids researchers in understanding their function as a path to disease prevention and therapeutics for conditions such as cancer, thrombosis, Alzheimer's disease and others. US-SOMO provides a convergence of experimental, computational, and modeling techniques, in which detailed molecular structure and properties are determined from data obtained in a range of experimental techniques that, by themselves, give incomplete information. Our goal in this work is to develop the infrastructure and user interfaces that will enable a wide range of scientists to carry out complicated experimental data analysis techniques on XSEDE. Our user community predominantly consists of biophysics and structural biology researchers. A recent search on PubMed reports 9,205 papers in the decade referencing the techniques we support. We believe our software will provide these researchers a convenient and unique framework to refine structures, thus advancing their research. The computed hydrodynamic parameters and scattering curves are screened against experimental data, effectively pruning potential structures into equivalence classes. Experimental methods may include analytical ultracentrifugation, dynamic light scattering, small angle X-ray and neutron scattering, NMR, fluorescence spectroscopy, and others. One source of macromolecular models is X-ray crystallography. However, the conformation in solution may not match that observed in the crystal form. Using computational techniques, an initial fixed model can be expanded into a search space utilizing high temperature molecular dynamic approaches or stochastic methods such as Brownian dynamics. The number of structures produced can vary greatly, ranging from hundreds to tens of thousands or more. This introduces a number of cyberinfrastructure challenges. Computing hydrodynamic parameters and small angle scattering curves can be computationally intensive for each structure, and therefore cluster compute resources are essential for timely results. Input and output data sizes can vary greatly from less than 1 MB to 2 GB or more. Although the parallelization is trivial, along with data size variability there is a large range of compute sizes, ranging from one to potentially thousands of cores with compute time of minutes to hours. In addition to the distributed computing infrastructure challenges, an important concern was how to allow a user to conveniently submit, monitor and retrieve results from within the C++/Qt GUI application while maintaining a method for authentication, approval and registered publication usage throttling. Middleware supporting these design goals has been integrated into the application with assistance from the Open Gateway Computing Environments (OGCE) collaboration team. The approach was tested on various XSEDE clusters and local compute resources. This paper reviews current US-SOMO functionality and implementation with a focus on the newly deployed cluster integration. en_US
dc.description.sponsorship This work was supported by NIH grant K25GM090154 to EB, NSF grant OCI-1032742 to MP, NSF grant TG-MCB070040N to BD, and NIH grant RR-022200 to BD en_US
dc.language.iso en_US en_US
dc.publisher ACM en_US
dc.rights Except where otherwise noted, the contents of this presentation are © the Trustees of Indiana University. This content is released under the Creative Commons Attribution 3.0 Unported license (http://creativecommons.org/licenses/by/3.0/). This license includes the following terms: You are free to share – to copy, distribute and transmit the work and to remix – to adapt the work under the following conditions: attribution – you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work. en_US
dc.rights.uri http://creativecommons.org/licenses/by/3.0/ en_US
dc.subject bead modeling en_US
dc.subject hydrodynamics en_US
dc.subject analytical ultracentrifugation en_US
dc.subject small angle scattering en_US
dc.subject structural biology en_US
dc.subject Apache open source community en_US
dc.subject Apache Rave en_US
dc.subject Apache Airavata en_US
dc.subject Open Gateway Computing Environment en_US
dc.title Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools en_US
dc.type Preprint en_US
dc.altmetrics.display true en_US


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Except where otherwise noted, the contents of this presentation are © the Trustees of Indiana University. This content is released under the Creative Commons Attribution 3.0 Unported license (http://creativecommons.org/licenses/by/3.0/). This license includes the following terms: You are free to share – to copy, distribute and transmit the work and to remix – to adapt the work under the following conditions: attribution – you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work. Except where otherwise noted, the contents of this presentation are © the Trustees of Indiana University. This content is released under the Creative Commons Attribution 3.0 Unported license (http://creativecommons.org/licenses/by/3.0/). This license includes the following terms: You are free to share – to copy, distribute and transmit the work and to remix – to adapt the work under the following conditions: attribution – you must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). For any reuse or distribution, you must make clear to others the license terms of this work.

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