UltraScan solution modeler: Integrated hydrodynamic parameter and small angle scattering computation and fitting tools

Emre Brookes, Raminderjeet Singh, Marlon Pierce, Suresh Marru, Borries Demeler, Mattia Rocco

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationProceedings of the XSEDE12 Conference
Subtitle of host publicationBridging from the eXtreme to the Campus and Beyond
DOIs
StatePublished - Aug 29 2012
Event1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond, XSEDE12 - Chicago, IL, United States
Duration: Jul 16 2012Jul 19 2012

Publication series

NameACM International Conference Proceeding Series

Other

Other1st Conference of the Extreme Science and Engineering Discovery Environment: Bridging from the eXtreme to the Campus and Beyond, XSEDE12
CountryUnited States
CityChicago, IL
Period7/16/127/19/12

Keywords

  • Apache Airavata
  • Apache Rave
  • Apache open source community
  • analytical ultracentrifugation
  • bead modeling
  • hydrodynamics
  • open gateway computing environment
  • small angle scattering
  • structural biology

ASJC Scopus subject areas

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

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  • Cite this

    Brookes, E., Singh, R., Pierce, M., Marru, S., Demeler, B., & Rocco, M. (2012). UltraScan solution modeler: Integrated hydrodynamic parameter and small angle scattering computation and fitting tools. In Proceedings of the XSEDE12 Conference: Bridging from the eXtreme to the Campus and Beyond (ACM International Conference Proceeding Series). https://doi.org/10.1145/2335755.2335839